Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin carboxyl-terminal hydrolase CYLD.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g5973 g5973.t1 TSS g5973.t1 13111511 13111511
chr_2 g5973 g5973.t1 isoform g5973.t1 13112492 13117401
chr_2 g5973 g5973.t1 exon g5973.t1.exon1 13112492 13113031
chr_2 g5973 g5973.t1 cds g5973.t1.CDS1 13112492 13113031
chr_2 g5973 g5973.t1 exon g5973.t1.exon2 13113652 13114636
chr_2 g5973 g5973.t1 cds g5973.t1.CDS2 13113652 13114636
chr_2 g5973 g5973.t1 exon g5973.t1.exon3 13115565 13116083
chr_2 g5973 g5973.t1 cds g5973.t1.CDS3 13115565 13116083
chr_2 g5973 g5973.t1 exon g5973.t1.exon4 13116145 13116518
chr_2 g5973 g5973.t1 cds g5973.t1.CDS4 13116145 13116518
chr_2 g5973 g5973.t1 exon g5973.t1.exon5 13116574 13116808
chr_2 g5973 g5973.t1 cds g5973.t1.CDS5 13116574 13116808
chr_2 g5973 g5973.t1 exon g5973.t1.exon6 13116869 13117401
chr_2 g5973 g5973.t1 cds g5973.t1.CDS6 13116869 13117401
chr_2 g5973 g5973.t1 TTS g5973.t1 NA NA

Sequences

>g5973.t1 Gene=g5973 Length=3186
ATGAATAAATATAAAGACACTACAATGGAGTTATCATCGCCTTATGCAATTGTAATCGAA
GATCGAGCTCATGCAATATTAAATATTCCTGATGCAGGACCAGAGCATAATATTGAATTA
TGTAGAGGCACAATGATTGAAATCATAAAACCAAGCAGTCAAAACTATTACACAATCATG
ATACATGATTATCATCAAAAGAATTTGGCGTTTGAAAACAATTTATATAAAATAAAAGCA
AGTGTTTTTTGCATTGTACCAAAAGAAATTTGGCCATTTCTTATTGCCATCACCGATTCA
ATTGATAGAGCAAATATTTCTATGGACGAAGCCTTCATCGATTATATACTAAATTTGAGA
ATCAAGGGTTTTGTTTCTGTCAATTCACAATACTTTGGTATGTGCCCTATTCGACAATCA
CTACAATTTTTACCAGATCGAGAGCCACGAGATAAATCAAATGAATATAATTGCATAATT
CGTTACATCGGACCTGTGAAAGAGATTGGTCCAGGCTACTTCTTTGGTTTAGAGCTATTG
AACCTTAATAAAGGACATTCACCACAAGAGTTGGAAATAAAAAGTTTTTCAAAAAATTAC
ATCGACTGTGATTCAAATCTTGCATTTATTTTACCAGTGAACTTCATTCGAAAACCAAAA
GGATTGAAAAAGAATTCAACTCGTTCGGCAATTGGGAACATCCTTTGTGGTCTAAAAGAA
AAAGTAAAACCACAAAAAAATACATTGACGAGACATTCCTATATAGATTCGTCCGTTACT
GATTCTGCCAGTGAACGTTCATCTTCTTCAACAAGCAAGCGTCCCTTGACACCAGAATTG
GTGAATGATAATAAGAATGGTATGATGAATGTTAATAAATTTCCATCGTCAATCTCTAGT
CCAAATTTGGCGAAACAAGACAGCGCTTCATCGTCAACTACAAGCGGTTCTGCAAGAGTC
ATTAGCAATAGTGGTTTCGATTTGATTAATTTGTCAGAGGATTACAGTCAAATTGTTGCA
GAACGTGAATCCAAAATGGAAGAAAGAAGAATGTTGGGCTCAAGAGGAACTCAAACATTG
AGTGGTGGAAGCAACAACATTGAATCACGTACGACTCCGAAAAGCAATAGAAAGAAGGCA
ATGCTACTTCCCGCACCAAATCGTGAAATTAAGCCATCTACAATTTTACGTTTGGAAGAT
CGTGACTTGATTGTAATTGATAAACAGGACATTAAAGAAGCAGTTCGAAATGAAAGTGAT
GTGATAATTGTTGATCCACCAACACTTCCACAGACACCGTCAGATAATCACACGGAATTG
AGTGACATTTTGGGCAGCGAGTGGCCAGAATCTGCCGGCGCGACTGCATCTATCTTAAAT
AGTGACAAAAAATCAAATAATATATCTCCATCAGCTATAAGCAGCAATGGTTATCGATCA
ATAGAAAGAAATAAGAGTGCTAACATTGCATCTCACTTCAACAGTTCAAAGACGCGTTAT
GAATCACAAAATGGCTATAAACGAAATATAAACGGAAGGCAATACGAGAATTTAGATCAA
GACTCTGTTTCGTCTTCAGATCAAATTTCAGAGTGTCTCGTTCCTTCACCTTTAATTGAC
ATTCCAGGAACAGCTCTTGAGCTGGGTTCACTTGTGGAAGTAGCTTTGGAAAACGGGAAA
ATAAATCTTCATGGTGTAATTCGTTGGATTGGACAGAAACATCAAGATCACGACTATAAA
ATGCCAAATGGATATAACAATACTAGTAGTAATAATTGTAATGAGTTAGTAGTTGGCGTT
GAATTAGATGAACCATGTAATGATCGTGGTTTAAGATTAACTGATGGTGTTTATAATGGC
CAGAGATGCTTTCGATGTCCTGATAGACGTGCAATTTTTGTTTCACCTAAGCAATGTACA
AAGGATCGTCGTTTTATTGATGAAGTCGGATCTAAAGCATCAACAATTCGATCAACAACA
CCAAGTGATGGTAAAGCTTTTGGAGCCGATTGTCCAATTATTGAAGGCTCTATTTCTGCT
TTAAAATTTGTAAATTATGATGATCTCGAGGCACATTGTGGAAAATTTAAAGGAATTCAG
GGACATCATAATTCTTGTTATCTAGACGCTACACTTTTTGCAATGTTTACTTTTACGAGC
GTCTTTGATTCTGTTTTATTTCGCCCACGAGAACCTGAAGACAATGATCAATATGAAGAG
GTTCAGCGTGTTTTGCGAGAAGAAATTGTTAATCCATTAAGGAAAAATTTATTCGTTCGA
GCTGATCGTGTAATGAAATTGAGAAAACTGCTTGATAAATTGACATCTGTTAAAGGACTT
ATTAATGAAGAAAAAGATCCAGAAGAATTTTTAAACAGCTTATTGGCTCAGATTTTAAGA
GCAGAACCGTTTCTAAAACTAAGCTCAGGATTGGACGCATATTTCTATCAACTATTTATT
GAAAAAGACGAAAAACTAACATTACCAACAGTTCAGCAACTTTTTGAGCAATCATTTTTG
ACATCAGATATTAAACTAAAAGAAGTTCCATCATGCTTGATTATTCAGATGCCACGTTTT
GGAAAGAATTTCAAAACCTATCCCCGAATACTTCCATCACAAGTGCTTGACGTCACAGAC
ATTATTGAGGATTCTCCACGACAATGTACAATTTGTGGAACGCTTGCTGAATTTGAATGC
AAGGAATGCTTTGGCGTGCTTCAGACTGGTTCTGGCTTAGAATCAACAGCTTTCTGCAAA
AAATGTCTGCAAACAGCACATTCACATCATAAACGTCAAAATCATACACCAAAAGCTTTA
TCCATTCCTCATGATTTTAAAATATTGTCAGAATACAATCAAGTGCCACGACTTTTCATG
GAACTATTTGCTGTAATTTGTATTGAAACATCACATTATGTGGCATTTGTAAAAGCAGGA
TCAGGTCTGGATTCACCTTGGGTGTTTTTCGATTCAATGGCTGATCGAAAGGGAGAACAA
AATGGCTACAACATACCTGAAATGATTCCGGTACCTGATTTACCACTATGGCTATCAGAG
GATGGCGCACGGCAACTTCACGAAGCAAATCTTCACGATAAGCACTTACCACCATTTGCA
AAACGACTTTTGTGCGATGCATCTTTAATGTTATATCAATCTACTGAAATGATGATGTAT
CGATAA

>g5973.t1 Gene=g5973 Length=1061
MNKYKDTTMELSSPYAIVIEDRAHAILNIPDAGPEHNIELCRGTMIEIIKPSSQNYYTIM
IHDYHQKNLAFENNLYKIKASVFCIVPKEIWPFLIAITDSIDRANISMDEAFIDYILNLR
IKGFVSVNSQYFGMCPIRQSLQFLPDREPRDKSNEYNCIIRYIGPVKEIGPGYFFGLELL
NLNKGHSPQELEIKSFSKNYIDCDSNLAFILPVNFIRKPKGLKKNSTRSAIGNILCGLKE
KVKPQKNTLTRHSYIDSSVTDSASERSSSSTSKRPLTPELVNDNKNGMMNVNKFPSSISS
PNLAKQDSASSSTTSGSARVISNSGFDLINLSEDYSQIVAERESKMEERRMLGSRGTQTL
SGGSNNIESRTTPKSNRKKAMLLPAPNREIKPSTILRLEDRDLIVIDKQDIKEAVRNESD
VIIVDPPTLPQTPSDNHTELSDILGSEWPESAGATASILNSDKKSNNISPSAISSNGYRS
IERNKSANIASHFNSSKTRYESQNGYKRNINGRQYENLDQDSVSSSDQISECLVPSPLID
IPGTALELGSLVEVALENGKINLHGVIRWIGQKHQDHDYKMPNGYNNTSSNNCNELVVGV
ELDEPCNDRGLRLTDGVYNGQRCFRCPDRRAIFVSPKQCTKDRRFIDEVGSKASTIRSTT
PSDGKAFGADCPIIEGSISALKFVNYDDLEAHCGKFKGIQGHHNSCYLDATLFAMFTFTS
VFDSVLFRPREPEDNDQYEEVQRVLREEIVNPLRKNLFVRADRVMKLRKLLDKLTSVKGL
INEEKDPEEFLNSLLAQILRAEPFLKLSSGLDAYFYQLFIEKDEKLTLPTVQQLFEQSFL
TSDIKLKEVPSCLIIQMPRFGKNFKTYPRILPSQVLDVTDIIEDSPRQCTICGTLAEFEC
KECFGVLQTGSGLESTAFCKKCLQTAHSHHKRQNHTPKALSIPHDFKILSEYNQVPRLFM
ELFAVICIETSHYVAFVKAGSGLDSPWVFFDSMADRKGEQNGYNIPEMIPVPDLPLWLSE
DGARQLHEANLHDKHLPPFAKRLLCDASLMLYQSTEMMMYR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g5973.t1 Gene3D G3DSA:2.30.30.190 - 538 655 2.4E-23
12 g5973.t1 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 688 1061 1.3E-166
11 g5973.t1 MobiDBLite mobidb-lite consensus disorder prediction 247 317 -
9 g5973.t1 MobiDBLite mobidb-lite consensus disorder prediction 248 317 -
10 g5973.t1 MobiDBLite mobidb-lite consensus disorder prediction 353 375 -
8 g5973.t1 MobiDBLite mobidb-lite consensus disorder prediction 354 371 -
3 g5973.t1 PANTHER PTHR11830:SF3 CYLINDROMATOSIS, ISOFORM D 91 1060 1.8E-210
4 g5973.t1 PANTHER PTHR11830 40S RIBOSOMAL PROTEIN S3A 91 1060 1.8E-210
2 g5973.t1 Pfam PF01302 CAP-Gly domain 560 639 2.1E-12
1 g5973.t1 Pfam PF00443 Ubiquitin carboxyl-terminal hydrolase 698 991 2.4E-7
14 g5973.t1 ProSiteProfiles PS50235 Ubiquitin specific protease (USP) domain profile. 697 1021 16.571
7 g5973.t1 SMART SM01052 CAP_GLY_2 548 640 2.2E-7
5 g5973.t1 SUPERFAMILY SSF74924 Cap-Gly domain 540 716 1.57E-20
6 g5973.t1 SUPERFAMILY SSF54001 Cysteine proteinases 693 991 4.12E-26

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5973/g5973.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5973.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004843 thiol-dependent deubiquitinase MF
GO:0016579 protein deubiquitination BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values