Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquitin carboxyl-terminal hydrolase 7.

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 g5270 g5270.t1 TSS g5270.t1 8331805 8331805
chr_2 g5270 g5270.t1 isoform g5270.t1 8331997 8335461
chr_2 g5270 g5270.t1 exon g5270.t1.exon1 8331997 8332024
chr_2 g5270 g5270.t1 cds g5270.t1.CDS1 8331997 8332024
chr_2 g5270 g5270.t1 exon g5270.t1.exon2 8332154 8332924
chr_2 g5270 g5270.t1 cds g5270.t1.CDS2 8332154 8332924
chr_2 g5270 g5270.t1 exon g5270.t1.exon3 8332986 8334544
chr_2 g5270 g5270.t1 cds g5270.t1.CDS3 8332986 8334544
chr_2 g5270 g5270.t1 exon g5270.t1.exon4 8334604 8335461
chr_2 g5270 g5270.t1 cds g5270.t1.CDS4 8334604 8335461
chr_2 g5270 g5270.t1 TTS g5270.t1 8336485 8336485

Sequences

>g5270.t1 Gene=g5270 Length=3216
ATGGAGACCGAAGAAAATGAAACTCCAGATATCACTCCTTCAGATCATAATATGGAGGAT
GAACTAAGAAGCGAGGCAACGTTTCAATTGACGATTGAAAACTTTAGTAAAATGTCTGAG
ACTATGCTCTCAGAGGCACATTATGTGCGTGGATTACCGTGGAAAATTATGGCTATGCCA
CGATCGTCGAATGACAAAGACAAAAGTTTAGGATTTTTCCTACAATGTAATGCCGAATGT
GACTCAAATTGGAACTGTTCTGCTACAGCAGATTTGCGTTTATTGAGTTTCAAAAAAGAA
ACACCGCCAGTTTCAAGAAAAATTAAACATGTCTTTTACAACAAGGAAAATGACTGGGGA
TTTTCAACCTTTCAATCTTTTGCTGACATTCTTGATCCAGAAAAAGGCTACATACAGAAT
GACACAATAGTTTTGGAAGTACATGTACAAGCGGAAGCACCGCATAATGCTTATTGGGAC
TCAAAGAAATTGACAGGATACGTTGGCCTTAAGAATCAGGGAGCAACTTGCTACATGAAT
TCTCTCTTGCAAACACTTTACTTCACAAATGAACTCAGAAAAGCTGTCTATAAAATGCCG
ACAGAGGCTGATGACAGCAGTAAATCCGTAGCTCTTGCATTACAAAGAGTATTTCATGAG
CTACAGTCGTCCAACAAGCCTGTTGGCACAAAAAAACTCACAAAAAGTTTTGGGTGGGAG
ACGCTCGACTCGTTTATGCAACATGATGTGCAAGAATTTTTACGTGTCCTTCTTGATAAG
TTAGAAATCAAAATGAAAGGTACTTCCATTGAAGGAACTATACCAAGATTATTTGCAGGT
AAAATGATTTCATTCATCAAATGCAAGAATGTCAACTACAAAAGTACCAAAACGGAGACC
TTTTATGATATTCAACTAAATATCAAGGGCAAAAAGAATGTTTATGAATCATTTGACGAT
TATGTATCTACGGAAATTTTAGACGATGAAAATAAGTATGATGCTGGTGAATATGGACTA
CAAAAGGCTGAAAAAGGTGTGATTTTTGCTTCGTTTCCACCCGTTTTGCATTTACATTTG
CTTCGCTTCCAATATGACCCTATGACAAACAATTCAGTCAAGTTTAATGATCGTTTTGAG
TTTCATGAGAAAATCAATTTAGATAAGTACTTGGAGAAACCAGAAGAAACACCAGCGAAT
TATATTTTGCATGCCGTACTAGTGCATTCAGGTGATAATCATGGGGGACATTATGTTGTT
TTCATTAATCCACGAGGTGATGGAAATTGGTGCAAATTTGATGATGATGTAGTTTCAGCT
GTTCCTAAAACAGCAGCAATTGATCAAAATTATGGCGGTACTGAAGATGATTTTATGCTT
AATGTGCGTAATTGTACAAACGCTTATATGTTGGTTTATGTACGTGAAGCACAAATGAAA
ACAATTCTTCAAGAAATCGCTGAAGAAGACATTCCCTCGGAGCTTAATGATAAATTAAAC
GAGGAAAAACGTATGGAAATGGCAAAACGAAAGGAACGCAATGAAGCATCAAATTACATC
AATGTAAATGTGATTTTGGAAGATTATTTTGATGGTCATCATGCAAACGATCTATTCAAT
CCTGACGCAACACATTATAGATGTTTTAAAATCAAACAAAATTCTCCGCTTCATGAGCTT
GTCAGTCTTATTCAAAGTACATTTAAAGTATCTCCTTTAAAAATGCGTTTATGGTCATTT
TCGTATATGGGTAGTCATAGTGGTGGACAAATGTATCATAACTCGACAAGTGGCAGTGGT
GGTTTACTCTCAAATGGTCTTTACAACATAGACATTAATGATCCCGAGTTATTAAACAAT
CCAGTTACATATTTATCACGCGACCATAATCCATGGACATTGTTTTTAGAAATGCCACCA
CCTGATCTTGAATGTGCTGCTCTGCCTCCATATTCGGCTAATGTTCACTTGCTTGTGTTC
TTCAAGTATTATGATCCTGTTAACAAATCACTGACATATGCCGGTTCACGAATTGTAGTA
CATGATGAAAAACTTATAGACCTTGTATCTGAGTTGAATGAACTTATTGGAATGCCGCCA
GATACTGCACTTGATTTTTACAAAACGAAAGTAAAAGTTGATCCGCATGTTCCAGTAGCA
ACACTAGCAAAGAACGGTGAAATATTTATTTTTGAACGTAATGAAAAGTTGCCGAATTTG
GAACTACCAACCTATCTCGACTATTATAATGATTTGCAATTTCGCGTAGAAGTCACTTTC
ATCGATAAGAACATTCAAAATGATAATGGATTCACAATTGAACTATCAATAAATTCAACT
TATGATCAAATGGCTAAAGCTGTCGGTCAACGAATTAATGTAGATCCATATGAGATTCAA
TTTTTCAAAAGTGTAAGCTATAAAGATATACCAGGTCCAGCCATAGCAGGTTCTTTCGAG
GGACAATTAAAGGACATTTTACAGAGCAAATCAAAAAATAGTAAAAAATTTTTATTCTAT
CAGCGACTTTCAATGAATATAAACGACTTGGAGGATAAGAAACCATTCAAGTGCATGTTC
CTTTTGCCGAGCAATAAAGATATGAAAGAAGTAACACTTTATCCACATAAGAATGGTACT
GTTAAAACACTTCTCGAAGAGGCGGCAAAAGTTGTTAAATTTAGTGATAGTAATAGCACT
AAGCGATTACGCATTTGCGAACAACACAGCTCTAAATTAATATGGCCAGGACCATCCGAA
AATACATCCTTAGATAAATTACAAGTTTATAGTGAGTCGGCAAGTCAAACTCAAACGCAA
AAGTTTCTGCGCATCGAAGAAGTACCAATGGACGAAATGGATATAGATGAGCAAATGGAA
GCTCTAGTTCCAGTGATTCATTTCCATAAAAATTTGTTTACAATGTTCGGTGTGCCGCTT
TTGATAAAAGTTTGCGACCAAGAAACCTATAAAGATGTAAAAAATCGTATTCAGAAAAAA
TTGAACATTTCGCAATACGAATGGGAGAAATATAAATTGGCAATTATTCAAAATAAATCA
GCTAATCCTGTTGACGATAATGACAAGGTGATTTTGGAAAAGTTTCAAGGTGATGAGAGC
TCTCGTTGTTTACTCGGACTTGATCATGCTAATAAGAGCGCCTATCCTACCACAAAACTG
AACATCTTTGAAAAGTCGATTAAGATTTATAATTAA

>g5270.t1 Gene=g5270 Length=1071
METEENETPDITPSDHNMEDELRSEATFQLTIENFSKMSETMLSEAHYVRGLPWKIMAMP
RSSNDKDKSLGFFLQCNAECDSNWNCSATADLRLLSFKKETPPVSRKIKHVFYNKENDWG
FSTFQSFADILDPEKGYIQNDTIVLEVHVQAEAPHNAYWDSKKLTGYVGLKNQGATCYMN
SLLQTLYFTNELRKAVYKMPTEADDSSKSVALALQRVFHELQSSNKPVGTKKLTKSFGWE
TLDSFMQHDVQEFLRVLLDKLEIKMKGTSIEGTIPRLFAGKMISFIKCKNVNYKSTKTET
FYDIQLNIKGKKNVYESFDDYVSTEILDDENKYDAGEYGLQKAEKGVIFASFPPVLHLHL
LRFQYDPMTNNSVKFNDRFEFHEKINLDKYLEKPEETPANYILHAVLVHSGDNHGGHYVV
FINPRGDGNWCKFDDDVVSAVPKTAAIDQNYGGTEDDFMLNVRNCTNAYMLVYVREAQMK
TILQEIAEEDIPSELNDKLNEEKRMEMAKRKERNEASNYINVNVILEDYFDGHHANDLFN
PDATHYRCFKIKQNSPLHELVSLIQSTFKVSPLKMRLWSFSYMGSHSGGQMYHNSTSGSG
GLLSNGLYNIDINDPELLNNPVTYLSRDHNPWTLFLEMPPPDLECAALPPYSANVHLLVF
FKYYDPVNKSLTYAGSRIVVHDEKLIDLVSELNELIGMPPDTALDFYKTKVKVDPHVPVA
TLAKNGEIFIFERNEKLPNLELPTYLDYYNDLQFRVEVTFIDKNIQNDNGFTIELSINST
YDQMAKAVGQRINVDPYEIQFFKSVSYKDIPGPAIAGSFEGQLKDILQSKSKNSKKFLFY
QRLSMNINDLEDKKPFKCMFLLPSNKDMKEVTLYPHKNGTVKTLLEEAAKVVKFSDSNST
KRLRICEQHSSKLIWPGPSENTSLDKLQVYSESASQTQTQKFLRIEEVPMDEMDIDEQME
ALVPVIHFHKNLFTMFGVPLLIKVCDQETYKDVKNRIQKKLNISQYEWEKYKLAIIQNKS
ANPVDDNDKVILEKFQGDESSRCLLGLDHANKSAYPTTKLNIFEKSIKIYN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g5270.t1 CDD cd03772 MATH_HAUSP 24 156 1.12298E-65
16 g5270.t1 CDD cd02659 peptidase_C19C 166 476 6.73684E-147
14 g5270.t1 Coils Coil Coil 495 515 -
13 g5270.t1 Gene3D G3DSA:2.60.210.10 Apoptosis 21 164 4.1E-41
12 g5270.t1 Gene3D G3DSA:3.90.70.10 Cysteine proteinases 165 478 4.7E-88
9 g5270.t1 Gene3D G3DSA:3.10.20.90 - 490 590 1.2E-24
11 g5270.t1 Gene3D G3DSA:3.10.20.90 - 649 754 1.6E-16
10 g5270.t1 Gene3D G3DSA:3.10.20.90 - 755 851 3.2E-36
20 g5270.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
5 g5270.t1 PANTHER PTHR24006:SF793 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7 14 928 0.0
6 g5270.t1 PANTHER PTHR24006 UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 14 928 0.0
1 g5270.t1 Pfam PF00917 MATH domain 32 150 1.6E-16
2 g5270.t1 Pfam PF00443 Ubiquitin carboxyl-terminal hydrolase 168 473 4.0E-49
3 g5270.t1 Pfam PF12436 ICP0-binding domain of Ubiquitin-specific protease 7 626 827 1.8E-43
4 g5270.t1 Pfam PF14533 Ubiquitin-specific protease C-terminal 838 1053 1.5E-53
19 g5270.t1 ProSitePatterns PS00972 Ubiquitin specific protease (USP) domain signature 1. 169 184 -
18 g5270.t1 ProSitePatterns PS00973 Ubiquitin specific protease (USP) domain signature 2. 401 418 -
21 g5270.t1 ProSiteProfiles PS50144 MATH/TRAF domain profile. 25 149 24.047
22 g5270.t1 ProSiteProfiles PS50235 Ubiquitin specific protease (USP) domain profile. 168 476 42.034
17 g5270.t1 SMART SM00061 math_3 30 130 9.0E-12
7 g5270.t1 SUPERFAMILY SSF49599 TRAF domain-like 25 152 4.91E-27
8 g5270.t1 SUPERFAMILY SSF54001 Cysteine proteinases 163 503 8.24E-97

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5270/g5270.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5270.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0004843 thiol-dependent deubiquitinase MF
GO:0006511 ubiquitin-dependent protein catabolic process BP
GO:0005515 protein binding 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