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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CIT-LYZ (FusionGDB2 ID:HG11113TG4069)

Fusion Gene Summary for CIT-LYZ

check button Fusion gene summary
Fusion gene informationFusion gene name: CIT-LYZ
Fusion gene ID: hg11113tg4069
HgeneTgene
Gene symbol

CIT

LYZ

Gene ID

11113

4069

Gene namecitron rho-interacting serine/threonine kinaselysozyme
SynonymsCITK|CRIK|MCPH17|STK21LYZF1|LZM
Cytomap('CIT')('LYZ')

12q24.23

12q15

Type of geneprotein-codingprotein-coding
Descriptioncitron Rho-interacting kinasecitron (rho-interacting, serine/threonine kinase 21)serine/threonine kinase 21serine/threonine-protein kinase 21lysozyme C1,4-beta-N-acetylmuramidase Cc-type lysozymelysozyme F1
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000261833, ENST00000392521, 
ENST00000537607, 
Fusion gene scores* DoF score9 X 9 X 6=48651 X 27 X 13=17901
# samples 960
** MAII scorelog2(9/486*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(60/17901*10)=-4.89893387178018
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CIT [Title/Abstract] AND LYZ [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCIT(120260624)-LYZ(69743888), # samples:2
Anticipated loss of major functional domain due to fusion event.CIT-LYZ seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CIT-LYZ seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CIT-LYZ seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CIT-LYZ seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CIT-LYZ seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
CIT-LYZ seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CIT-LYZ seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneLYZ

GO:0031640

killing of cells of other organism

9727055

TgeneLYZ

GO:0042742

defense response to bacterium

21093056

TgeneLYZ

GO:0050830

defense response to Gram-positive bacterium

21093056


check buttonFusion gene breakpoints across CIT (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across LYZ (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4SARCTCGA-3B-A9HO-01ACITchr12

120260624

-LYZchr12

69743888

+


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Fusion Gene ORF analysis for CIT-LYZ

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000261833ENST00000261267CITchr12

120260624

-LYZchr12

69743888

+
Frame-shiftENST00000261833ENST00000549690CITchr12

120260624

-LYZchr12

69743888

+
Frame-shiftENST00000392521ENST00000261267CITchr12

120260624

-LYZchr12

69743888

+
Frame-shiftENST00000392521ENST00000549690CITchr12

120260624

-LYZchr12

69743888

+
In-frameENST00000261833ENST00000548839CITchr12

120260624

-LYZchr12

69743888

+
In-frameENST00000392521ENST00000548839CITchr12

120260624

-LYZchr12

69743888

+
intron-3CDSENST00000537607ENST00000261267CITchr12

120260624

-LYZchr12

69743888

+
intron-3CDSENST00000537607ENST00000548839CITchr12

120260624

-LYZchr12

69743888

+
intron-3CDSENST00000537607ENST00000549690CITchr12

120260624

-LYZchr12

69743888

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000392521CITchr12120260624-ENST00000548839LYZchr1269743888+15661167261345439
ENST00000261833CITchr12120260624-ENST00000548839LYZchr1269743888+15631164231342439

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000392521ENST00000548839CITchr12120260624-LYZchr1269743888+0.0013517840.9986482
ENST00000261833ENST00000548839CITchr12120260624-LYZchr1269743888+0.0013562380.9986438

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Fusion Genomic Features for CIT-LYZ


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
CITchr12120260623-LYZchr1269743887+0.0006025440.9993974
CITchr12120260623-LYZchr1269743887+0.0006025440.9993974

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.
genomic feature

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for CIT-LYZ


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:120260624/chr12:69743888)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCITchr12:120260624chr12:69743888ENST00000261833-94797_3603702028.0DomainProtein kinase
HgeneCITchr12:120260624chr12:69743888ENST00000392521-94897_3603702070.0DomainProtein kinase
HgeneCITchr12:120260624chr12:69743888ENST00000261833-947103_1113702028.0Nucleotide bindingATP
HgeneCITchr12:120260624chr12:69743888ENST00000392521-948103_1113702070.0Nucleotide bindingATP

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCITchr12:120260624chr12:69743888ENST00000261833-947453_12973702028.0Coiled coilOntology_term=ECO:0000255
HgeneCITchr12:120260624chr12:69743888ENST00000392521-948453_12973702070.0Coiled coilOntology_term=ECO:0000255
HgeneCITchr12:120260624chr12:69743888ENST00000261833-9471443_15633702028.0DomainPH
HgeneCITchr12:120260624chr12:69743888ENST00000261833-9471591_18813702028.0DomainCNH
HgeneCITchr12:120260624chr12:69743888ENST00000261833-947361_4313702028.0DomainAGC-kinase C-terminal
HgeneCITchr12:120260624chr12:69743888ENST00000392521-9481443_15633702070.0DomainPH
HgeneCITchr12:120260624chr12:69743888ENST00000392521-9481591_18813702070.0DomainCNH
HgeneCITchr12:120260624chr12:69743888ENST00000392521-948361_4313702070.0DomainAGC-kinase C-terminal
HgeneCITchr12:120260624chr12:69743888ENST00000261833-9471953_19583702028.0MotifSH3-binding
HgeneCITchr12:120260624chr12:69743888ENST00000392521-9481953_19583702070.0MotifSH3-binding
HgeneCITchr12:120260624chr12:69743888ENST00000261833-9471362_14113702028.0Zinc fingerPhorbol-ester/DAG-type
HgeneCITchr12:120260624chr12:69743888ENST00000392521-9481362_14113702070.0Zinc fingerPhorbol-ester/DAG-type
TgeneLYZchr12:120260624chr12:69743888ENST000002612670419_14845149.0DomainC-type lysozyme


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Fusion Gene Sequence for CIT-LYZ


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>16870_16870_1_CIT-LYZ_CIT_chr12_120260624_ENST00000261833_LYZ_chr12_69743888_ENST00000548839_length(transcript)=1563nt_BP=1164nt
GCGGGGCGGAACAGATCGCAGACCTGGGGGTTCGCAGAGCCGCCAGTGGGGAGATGTTGAAGTTCAAATATGGAGCGCGGAATCCTTTGG
ATGCTGGTGCTGCTGAACCCATTGCCAGCCGGGCCTCCAGGCTGAATCTGTTCTTCCAGGGGAAACCACCCTTTATGACTCAACAGCAGA
TGTCTCCTCTTTCCCGAGAAGGGATATTAGATGCCCTCTTTGTTCTCTTTGAAGAATGCAGTCAGCCTGCTCTGATGAAGATTAAGCACG
TGAGCAACTTTGTCCGGAAGTATTCCGACACCATAGCTGAGTTACAGGAGCTCCAGCCTTCGGCAAAGGACTTCGAAGTCAGAAGTCTTG
TAGGTTGTGGTCACTTTGCTGAAGTGCAGGTGGTAAGAGAGAAAGCAACCGGGGACATCTATGCTATGAAAGTGATGAAGAAGAAGGCTT
TATTGGCCCAGGAGCAGGTTTCATTTTTTGAGGAAGAGCGGAACATATTATCTCGAAGCACAAGCCCGTGGATCCCCCAATTACAGTATG
CCTTTCAGGACAAAAATCACCTTTATCTGGTCATGGAATATCAGCCTGGAGGGGACTTGCTGTCACTTTTGAATAGATATGAGGACCAGT
TAGATGAAAACCTGATACAGTTTTACCTAGCTGAGCTGATTTTGGCTGTTCACAGCGTTCATCTGATGGGATACGTGCATCGAGACATCA
AGCCTGAGAACATTCTCGTTGACCGCACAGGACACATCAAGCTGGTGGATTTTGGATCTGCCGCGAAAATGAATTCAAACAAGATGGTGA
ATGCCAAACTCCCGATTGGGACCCCAGATTACATGGCTCCTGAAGTGCTGACTGTGATGAACGGGGATGGAAAAGGCACCTACGGCCTGG
ACTGTGACTGGTGGTCAGTGGGCGTGATTGCCTATGAGATGATTTATGGGAGATCCCCCTTCGCAGAGGGAACCTCTGCCAGAACCTTCA
ATAACATTATGAATTTCCAGCGGTTTTTGAAATTTCCAGATGACCCCAAAGTGAGCAGTGACTTTCTTGATCTGATTCAAAGCTTGTTGT
GCGGCCAGAAAGAGAGACTGAAGTTTGAAGGTCTTTGCTGCCATCCTTTCTTCTCTAAAATTGACTGGAACAACATTCGTAACTGGATGT
GTTTGGCCAAATGGGAGAGTGGTTACAACACACGAGCTACAAACTACAATGCTGGAGACAGAAGCACTGATTATGGGATATTTCAGATCA
ATAGCCGCTACTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATTTATCCTGCAGTGGTAAGACAAGCTAATATTTGA
CCAATCTGGTTATACTTACAAGAATTGAGACTCAATACAAATGAAAAAGCCTTGAAAGGTTCATGAGGGACCTAGAAAAACTACATCTCA
ACTTCCAGAAAGTCATTATTATTTTCCTCATAATTCCCTGAGTAAGAAATTAAAGAAGTGGTATCATAAAAGGTTGATGTTTTTTAATAT

>16870_16870_1_CIT-LYZ_CIT_chr12_120260624_ENST00000261833_LYZ_chr12_69743888_ENST00000548839_length(amino acids)=439AA_BP=381
MGVRRAASGEMLKFKYGARNPLDAGAAEPIASRASRLNLFFQGKPPFMTQQQMSPLSREGILDALFVLFEECSQPALMKIKHVSNFVRKY
SDTIAELQELQPSAKDFEVRSLVGCGHFAEVQVVREKATGDIYAMKVMKKKALLAQEQVSFFEEERNILSRSTSPWIPQLQYAFQDKNHL
YLVMEYQPGGDLLSLLNRYEDQLDENLIQFYLAELILAVHSVHLMGYVHRDIKPENILVDRTGHIKLVDFGSAAKMNSNKMVNAKLPIGT
PDYMAPEVLTVMNGDGKGTYGLDCDWWSVGVIAYEMIYGRSPFAEGTSARTFNNIMNFQRFLKFPDDPKVSSDFLDLIQSLLCGQKERLK

--------------------------------------------------------------
>16870_16870_2_CIT-LYZ_CIT_chr12_120260624_ENST00000392521_LYZ_chr12_69743888_ENST00000548839_length(transcript)=1566nt_BP=1167nt
GGCGCGGGGCGGAACAGATCGCAGACCTGGGGGTTCGCAGAGCCGCCAGTGGGGAGATGTTGAAGTTCAAATATGGAGCGCGGAATCCTT
TGGATGCTGGTGCTGCTGAACCCATTGCCAGCCGGGCCTCCAGGCTGAATCTGTTCTTCCAGGGGAAACCACCCTTTATGACTCAACAGC
AGATGTCTCCTCTTTCCCGAGAAGGGATATTAGATGCCCTCTTTGTTCTCTTTGAAGAATGCAGTCAGCCTGCTCTGATGAAGATTAAGC
ACGTGAGCAACTTTGTCCGGAAGTATTCCGACACCATAGCTGAGTTACAGGAGCTCCAGCCTTCGGCAAAGGACTTCGAAGTCAGAAGTC
TTGTAGGTTGTGGTCACTTTGCTGAAGTGCAGGTGGTAAGAGAGAAAGCAACCGGGGACATCTATGCTATGAAAGTGATGAAGAAGAAGG
CTTTATTGGCCCAGGAGCAGGTTTCATTTTTTGAGGAAGAGCGGAACATATTATCTCGAAGCACAAGCCCGTGGATCCCCCAATTACAGT
ATGCCTTTCAGGACAAAAATCACCTTTATCTGGTCATGGAATATCAGCCTGGAGGGGACTTGCTGTCACTTTTGAATAGATATGAGGACC
AGTTAGATGAAAACCTGATACAGTTTTACCTAGCTGAGCTGATTTTGGCTGTTCACAGCGTTCATCTGATGGGATACGTGCATCGAGACA
TCAAGCCTGAGAACATTCTCGTTGACCGCACAGGACACATCAAGCTGGTGGATTTTGGATCTGCCGCGAAAATGAATTCAAACAAGATGG
TGAATGCCAAACTCCCGATTGGGACCCCAGATTACATGGCTCCTGAAGTGCTGACTGTGATGAACGGGGATGGAAAAGGCACCTACGGCC
TGGACTGTGACTGGTGGTCAGTGGGCGTGATTGCCTATGAGATGATTTATGGGAGATCCCCCTTCGCAGAGGGAACCTCTGCCAGAACCT
TCAATAACATTATGAATTTCCAGCGGTTTTTGAAATTTCCAGATGACCCCAAAGTGAGCAGTGACTTTCTTGATCTGATTCAAAGCTTGT
TGTGCGGCCAGAAAGAGAGACTGAAGTTTGAAGGTCTTTGCTGCCATCCTTTCTTCTCTAAAATTGACTGGAACAACATTCGTAACTGGA
TGTGTTTGGCCAAATGGGAGAGTGGTTACAACACACGAGCTACAAACTACAATGCTGGAGACAGAAGCACTGATTATGGGATATTTCAGA
TCAATAGCCGCTACTGGTGTAATGATGGCAAAACCCCAGGAGCAGTTAATGCCTGTCATTTATCCTGCAGTGGTAAGACAAGCTAATATT
TGACCAATCTGGTTATACTTACAAGAATTGAGACTCAATACAAATGAAAAAGCCTTGAAAGGTTCATGAGGGACCTAGAAAAACTACATC
TCAACTTCCAGAAAGTCATTATTATTTTCCTCATAATTCCCTGAGTAAGAAATTAAAGAAGTGGTATCATAAAAGGTTGATGTTTTTTAA

>16870_16870_2_CIT-LYZ_CIT_chr12_120260624_ENST00000392521_LYZ_chr12_69743888_ENST00000548839_length(amino acids)=439AA_BP=381
MGVRRAASGEMLKFKYGARNPLDAGAAEPIASRASRLNLFFQGKPPFMTQQQMSPLSREGILDALFVLFEECSQPALMKIKHVSNFVRKY
SDTIAELQELQPSAKDFEVRSLVGCGHFAEVQVVREKATGDIYAMKVMKKKALLAQEQVSFFEEERNILSRSTSPWIPQLQYAFQDKNHL
YLVMEYQPGGDLLSLLNRYEDQLDENLIQFYLAELILAVHSVHLMGYVHRDIKPENILVDRTGHIKLVDFGSAAKMNSNKMVNAKLPIGT
PDYMAPEVLTVMNGDGKGTYGLDCDWWSVGVIAYEMIYGRSPFAEGTSARTFNNIMNFQRFLKFPDDPKVSSDFLDLIQSLLCGQKERLK

--------------------------------------------------------------

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Fusion Gene PPI Analysis for CIT-LYZ


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneCITchr12:120260624chr12:69743888ENST00000261833-9471091_1302370.33333333333332028.0Rho/Rac
HgeneCITchr12:120260624chr12:69743888ENST00000392521-9481091_1302370.33333333333332070.0Rho/Rac


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for CIT-LYZ


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CIT-LYZ


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCITC4310723MICROCEPHALY 17, PRIMARY, AUTOSOMAL RECESSIVE4CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCITC3711387Autosomal Recessive Primary Microcephaly1ORPHANET
HgeneCITC3809431MICROCEPHALY 11, PRIMARY, AUTOSOMAL RECESSIVE1GENOMICS_ENGLAND
TgeneC0268389Amyloidosis, familial visceral4CTD_human;GENOMICS_ENGLAND;UNIPROT