Gene loci information

Transcript annotation

  • This transcript has been annotated as Ubiquilin-1.

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_3 g3004 g3004.t11 TSS g3004.t11 21915593 21915593
chr_3 g3004 g3004.t11 isoform g3004.t11 21916395 21918043
chr_3 g3004 g3004.t11 exon g3004.t11.exon1 21916395 21917599
chr_3 g3004 g3004.t11 cds g3004.t11.CDS1 21916528 21917599
chr_3 g3004 g3004.t11 exon g3004.t11.exon2 21917663 21918043
chr_3 g3004 g3004.t11 cds g3004.t11.CDS2 21917663 21917739
chr_3 g3004 g3004.t11 TTS g3004.t11 21918308 21918308

Sequences

>g3004.t11 Gene=g3004 Length=1586
CAAAGCTCCACCAAAACCTGAAGCAGAAGGTCCAACACGACGACCAGCAGACGTACGTCA
AACACCATTCGGTTTAAATCAAATTGGTGGTCTATCAGGACTTGAAGCGCTCGGTGCTAA
TTCAAGTACATTCATGGATATGCAATCTCGAATGCAGCATGAATTGATGGGGAATCCTGA
GTTAATGAGAACAATTTTAGATAACCCCTTAGTTCAACAAATGCTTAATAATCCAGACAC
AATGAGAACCTTAATTACGAGCAATCCTCAAATGCAAGATTTAATGCAGCGTAATCCAGA
AATTTCTCACATGCTCAATAATCCCGAATTGTTGCGACAAACTATGGAACTTGCAAGGAA
TCCAGCTATGTTGCAAGAGTTGATGCGTTCACACGATAGAGCAATGTCTAATTTGGAATC
AGTTCCAGGTGGTTATAATGCGCTACATCGCATTTATCGTGATATTCAAGAGCCAATGCT
GAATGCAGCTTCTGGAGCATTTTCATCAAACCCATTCAGTGGATTAGTTGATAATGGAGG
TTCTGAGAATCCTCAACAAGGAAGTGAAAATCGTGAACCATTACCAAATCCATGGGGCGG
TAGTGGAAATCAAAATTCCCGACCAGCTCCACCACCAAATAATATTTTAAACACTCCAGC
AATGCAAAGTCTTTTACAACAAATGGGAGAAAATCCTGAAATGATGTCAACTATGATGAA
TGCACCATATATGCGTTCAATGATGGAAGCACTTTCACAAGATCCGAATATGGCGGCAAA
TTTGATTAGTCAAAGTCCTCTTCTTCAAGCAAATCCACAATTGCAAGATCAAATGAGAAC
AATGATGCCGCAACTTTTACAGCAAATGCAAAATCCAGAAGTTCAAAATATGCTGTCCAA
TCCTGATGCATTGAATGCAATCTTACAAATTCAACAAGGCATGGAACAACTTCGACAAGC
GGCACCAGGATTAGTTGGAACCATGGGAATTCCACCACCTCCTCCCGGAACGAATCAGCC
ACCACAAACTGGAAACACACCGAATGCACCAAATCAACAACTTTTTAATGACTTTATGCA
ACGAATGCTTAATGGAATGACCAATCAAGGAACACAACAGAATTTACCACCAGAACAGCG
ATATCAGTCGCAACTTGAGCAGCTTTCAGCTATGGGATTTGTAAATCGTGAAGCCAATTT
ACAAGCATTAATCGCGACATTCGGAGACATAAATGCAGCAGTTGAACGATTGTTGGCATT
GGGATCATTGTCATTAAGTTAACTTAATTAAATGGACGGTAAGATAAAGGAAGCAAAAGA
ATTAGAGTGGATGATATAAAAAATTTACCCTTTCCCAATCAACACAATATATATATATAT
ATATACACATTTATTTCTATTGATCTTCTCATTCTCTTCAGTTATTCAAATAAGTTTATT
TTATGAAAAAAAAAAATACATTTCAAAATTTTCCTTTCTTATAATTTTTTCTTTTCTATA
AATAATTATTTAGAATATGAGACATTATTGCTAAATTTATATGATATGTAAATTAAAAAA
TGGGGAAAAAATATTTGGAGTTGAAA

>g3004.t11 Gene=g3004 Length=382
MDMQSRMQHELMGNPELMRTILDNPLVQQMLNNPDTMRTLITSNPQMQDLMQRNPEISHM
LNNPELLRQTMELARNPAMLQELMRSHDRAMSNLESVPGGYNALHRIYRDIQEPMLNAAS
GAFSSNPFSGLVDNGGSENPQQGSENREPLPNPWGGSGNQNSRPAPPPNNILNTPAMQSL
LQQMGENPEMMSTMMNAPYMRSMMEALSQDPNMAANLISQSPLLQANPQLQDQMRTMMPQ
LLQQMQNPEVQNMLSNPDALNAILQIQQGMEQLRQAAPGLVGTMGIPPPPPGTNQPPQTG
NTPNAPNQQLFNDFMQRMLNGMTNQGTQQNLPPEQRYQSQLEQLSAMGFVNREANLQALI
ATFGDINAAVERLLALGSLSLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g3004.t11 CDD cd14399 UBA_PLICs 336 372 0.0000000
12 g3004.t11 Gene3D G3DSA:1.10.260.100 - 46 100 0.0000002
13 g3004.t11 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 320 380 0.0000000
2 g3004.t11 PANTHER PTHR10677 UBIQUILIN 1 163 0.0000000
4 g3004.t11 PANTHER PTHR10677:SF21 UBIQUILIN-4 1 163 0.0000000
3 g3004.t11 PANTHER PTHR10677 UBIQUILIN 167 375 0.0000000
5 g3004.t11 PANTHER PTHR10677:SF21 UBIQUILIN-4 167 375 0.0000000
1 g3004.t11 Pfam PF00627 UBA/TS-N domain 337 373 0.0000000
14 g3004.t11 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 332 376 11.8720000
8 g3004.t11 SMART SM00727 CBM 14 43 12.0000000
10 g3004.t11 SMART SM00727 CBM 44 83 0.0000000
11 g3004.t11 SMART SM00727 CBM 187 234 0.0000240
9 g3004.t11 SMART SM00727 CBM 238 270 0.6000000
7 g3004.t11 SMART SM00165 uba_6 337 375 0.0000002
6 g3004.t11 SUPERFAMILY SSF46934 UBA-like 322 374 0.0000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

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