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.t6 TSS g3004.t6 21915593 21915593
chr_3 g3004 g3004.t6 isoform g3004.t6 21915821 21918130
chr_3 g3004 g3004.t6 exon g3004.t6.exon1 21915821 21916329
chr_3 g3004 g3004.t6 cds g3004.t6.CDS1 21916270 21916329
chr_3 g3004 g3004.t6 exon g3004.t6.exon2 21916390 21917599
chr_3 g3004 g3004.t6 cds g3004.t6.CDS2 21916390 21917599
chr_3 g3004 g3004.t6 exon g3004.t6.exon3 21917663 21917755
chr_3 g3004 g3004.t6 cds g3004.t6.CDS3 21917663 21917739
chr_3 g3004 g3004.t6 exon g3004.t6.exon4 21918127 21918130
chr_3 g3004 g3004.t6 TTS g3004.t6 21918308 21918308

Sequences

>g3004.t6 Gene=g3004 Length=1816
ATGGCAGAAGGATCATCAAATCGTATTACGATAACAGTAAAAACACCTAAGGATAAGAAA
GATGTTGAAGTTGAAGAAGATTCTACAGTAGAGAAGGTAAAAATTCGAAAAATGAAATTT
ATCCTTGGAATTTTATTTTTTACACGTCTGTCACAACTAATCTTATGAAATACAATTCCA
AGTATTTCTTAATCATGTTTTTGTGTCAGATTAACATTTAAATGGTCATTTGGGTAACTC
TGACGTCATTTATAAGGAAAAATTGAAAAATTCGGTACACTATCACACACTACTATCATC
TATCTCTTTTTGCTTTATGTATTTATCAATTATGCATACTCATCGTCGTTTTTCTGTTTA
TTCGCTTATATTTCTAGTTCAAAGTTCTTGTTGCTGAAAAGTTTGAAGCTGAAGTTGAGC
AATTGTGCTTGATTTTTGCTGGAAAAATTATGAAAGATGCAGACACTCTTAAAAGTCACA
ATATAAAAGACGGATTGACAGTTCATTTGGTTATCAAAGCTCCACCAAAACCTGAAGCAG
AAGGTCCAACACGACGACCAGCAGACGTACGTCAAACACCATTCGGTTTAAATCAAATTG
GTGGTCTATCAGGACTTGAAGCGCTCGGTGCTAATTCAAGTACATTCATGGATATGCAAT
CTCGAATGCAGCATGAATTGATGGGGAATCCTGAGTTAATGAGAACAATTTTAGATAACC
CCTTAGTTCAACAAATGCTTAATAATCCAGACACAATGAGAACCTTAATTACGAGCAATC
CTCAAATGCAAGATTTAATGCAGCGTAATCCAGAAATTTCTCACATGCTCAATAATCCCG
AATTGTTGCGACAAACTATGGAACTTGCAAGGAATCCAGCTATGTTGCAAGAGTTGATGC
GTTCACACGATAGAGCAATGTCTAATTTGGAATCAGTTCCAGGTGGTTATAATGCGCTAC
ATCGCATTTATCGTGATATTCAAGAGCCAATGCTGAATGCAGCTTCTGGAGCATTTTCAT
CAAACCCATTCAGTGGATTAGTTGATAATGGAGGTTCTGAGAATCCTCAACAAGGAAGTG
AAAATCGTGAACCATTACCAAATCCATGGGGCGGTAGTGGAAATCAAAATTCCCGACCAG
CTCCACCACCAAATAATATTTTAAACACTCCAGCAATGCAAAGTCTTTTACAACAAATGG
GAGAAAATCCTGAAATGATGTCAACTATGATGAATGCACCATATATGCGTTCAATGATGG
AAGCACTTTCACAAGATCCGAATATGGCGGCAAATTTGATTAGTCAAAGTCCTCTTCTTC
AAGCAAATCCACAATTGCAAGATCAAATGAGAACAATGATGCCGCAACTTTTACAGCAAA
TGCAAAATCCAGAAGTTCAAAATATGCTGTCCAATCCTGATGCATTGAATGCAATCTTAC
AAATTCAACAAGGCATGGAACAACTTCGACAAGCGGCACCAGGATTAGTTGGAACCATGG
GAATTCCACCACCTCCTCCCGGAACGAATCAGCCACCACAAACTGGAAACACACCGAATG
CACCAAATCAACAACTTTTTAATGACTTTATGCAACGAATGCTTAATGGAATGACCAATC
AAGGAACACAACAGAATTTACCACCAGAACAGCGATATCAGTCGCAACTTGAGCAGCTTT
CAGCTATGGGATTTGTAAATCGTGAAGCCAATTTACAAGCATTAATCGCGACATTCGGAG
ACATAAATGCAGCAGTTGAACGATTGTTGGCATTGGGATCATTGTCATTAAGTTAACTTA
ATTAAATGGACGGACA

>g3004.t6 Gene=g3004 Length=448
MKDADTLKSHNIKDGLTVHLVIKAPPKPEAEGPTRRPADVRQTPFGLNQIGGLSGLEALG
ANSSTFMDMQSRMQHELMGNPELMRTILDNPLVQQMLNNPDTMRTLITSNPQMQDLMQRN
PEISHMLNNPELLRQTMELARNPAMLQELMRSHDRAMSNLESVPGGYNALHRIYRDIQEP
MLNAASGAFSSNPFSGLVDNGGSENPQQGSENREPLPNPWGGSGNQNSRPAPPPNNILNT
PAMQSLLQQMGENPEMMSTMMNAPYMRSMMEALSQDPNMAANLISQSPLLQANPQLQDQM
RTMMPQLLQQMQNPEVQNMLSNPDALNAILQIQQGMEQLRQAAPGLVGTMGIPPPPPGTN
QPPQTGNTPNAPNQQLFNDFMQRMLNGMTNQGTQQNLPPEQRYQSQLEQLSAMGFVNREA
NLQALIATFGDINAAVERLLALGSLSLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g3004.t6 CDD cd14399 UBA_PLICs 402 438 0.0000000
14 g3004.t6 Gene3D G3DSA:1.10.260.100 - 112 166 0.0000003
15 g3004.t6 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 386 446 0.0000000
3 g3004.t6 PANTHER PTHR10677 UBIQUILIN 1 31 0.0000000
6 g3004.t6 PANTHER PTHR10677:SF21 UBIQUILIN-4 1 31 0.0000000
4 g3004.t6 PANTHER PTHR10677 UBIQUILIN 47 229 0.0000000
7 g3004.t6 PANTHER PTHR10677:SF21 UBIQUILIN-4 47 229 0.0000000
2 g3004.t6 PANTHER PTHR10677 UBIQUILIN 233 441 0.0000000
5 g3004.t6 PANTHER PTHR10677:SF21 UBIQUILIN-4 233 441 0.0000000
1 g3004.t6 Pfam PF00627 UBA/TS-N domain 403 439 0.0000000
16 g3004.t6 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 398 442 11.8720000
11 g3004.t6 SMART SM00727 CBM 80 109 12.0000000
10 g3004.t6 SMART SM00727 CBM 110 149 0.0000000
13 g3004.t6 SMART SM00727 CBM 253 300 0.0000240
12 g3004.t6 SMART SM00727 CBM 304 336 0.6000000
9 g3004.t6 SMART SM00165 uba_6 403 441 0.0000002
8 g3004.t6 SUPERFAMILY SSF46934 UBA-like 388 440 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