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.t1 TSS g3004.t1 21915593 21915593
chr_3 g3004 g3004.t1 isoform g3004.t1 21915821 21917739
chr_3 g3004 g3004.t1 exon g3004.t1.exon1 21915821 21915916
chr_3 g3004 g3004.t1 cds g3004.t1.CDS1 21915821 21915916
chr_3 g3004 g3004.t1 exon g3004.t1.exon2 21916198 21916329
chr_3 g3004 g3004.t1 cds g3004.t1.CDS2 21916198 21916329
chr_3 g3004 g3004.t1 exon g3004.t1.exon3 21916390 21917599
chr_3 g3004 g3004.t1 cds g3004.t1.CDS3 21916390 21917599
chr_3 g3004 g3004.t1 exon g3004.t1.exon4 21917663 21917739
chr_3 g3004 g3004.t1 cds g3004.t1.CDS4 21917663 21917739
chr_3 g3004 g3004.t1 TTS g3004.t1 21918308 21918308

Sequences

>g3004.t1 Gene=g3004 Length=1515
ATGGCAGAAGGATCATCAAATCGTATTACGATAACAGTAAAAACACCTAAGGATAAGAAA
GATGTTGAAGTTGAAGAAGATTCTACAGTAGAGAAGTTCAAAGTTCTTGTTGCTGAAAAG
TTTGAAGCTGAAGTTGAGCAATTGTGCTTGATTTTTGCTGGAAAAATTATGAAAGATGCA
GACACTCTTAAAAGTCACAATATAAAAGACGGATTGACAGTTCATTTGGTTATCAAAGCT
CCACCAAAACCTGAAGCAGAAGGTCCAACACGACGACCAGCAGACGTACGTCAAACACCA
TTCGGTTTAAATCAAATTGGTGGTCTATCAGGACTTGAAGCGCTCGGTGCTAATTCAAGT
ACATTCATGGATATGCAATCTCGAATGCAGCATGAATTGATGGGGAATCCTGAGTTAATG
AGAACAATTTTAGATAACCCCTTAGTTCAACAAATGCTTAATAATCCAGACACAATGAGA
ACCTTAATTACGAGCAATCCTCAAATGCAAGATTTAATGCAGCGTAATCCAGAAATTTCT
CACATGCTCAATAATCCCGAATTGTTGCGACAAACTATGGAACTTGCAAGGAATCCAGCT
ATGTTGCAAGAGTTGATGCGTTCACACGATAGAGCAATGTCTAATTTGGAATCAGTTCCA
GGTGGTTATAATGCGCTACATCGCATTTATCGTGATATTCAAGAGCCAATGCTGAATGCA
GCTTCTGGAGCATTTTCATCAAACCCATTCAGTGGATTAGTTGATAATGGAGGTTCTGAG
AATCCTCAACAAGGAAGTGAAAATCGTGAACCATTACCAAATCCATGGGGCGGTAGTGGA
AATCAAAATTCCCGACCAGCTCCACCACCAAATAATATTTTAAACACTCCAGCAATGCAA
AGTCTTTTACAACAAATGGGAGAAAATCCTGAAATGATGTCAACTATGATGAATGCACCA
TATATGCGTTCAATGATGGAAGCACTTTCACAAGATCCGAATATGGCGGCAAATTTGATT
AGTCAAAGTCCTCTTCTTCAAGCAAATCCACAATTGCAAGATCAAATGAGAACAATGATG
CCGCAACTTTTACAGCAAATGCAAAATCCAGAAGTTCAAAATATGCTGTCCAATCCTGAT
GCATTGAATGCAATCTTACAAATTCAACAAGGCATGGAACAACTTCGACAAGCGGCACCA
GGATTAGTTGGAACCATGGGAATTCCACCACCTCCTCCCGGAACGAATCAGCCACCACAA
ACTGGAAACACACCGAATGCACCAAATCAACAACTTTTTAATGACTTTATGCAACGAATG
CTTAATGGAATGACCAATCAAGGAACACAACAGAATTTACCACCAGAACAGCGATATCAG
TCGCAACTTGAGCAGCTTTCAGCTATGGGATTTGTAAATCGTGAAGCCAATTTACAAGCA
TTAATCGCGACATTCGGAGACATAAATGCAGCAGTTGAACGATTGTTGGCATTGGGATCA
TTGTCATTAAGTTAA

>g3004.t1 Gene=g3004 Length=504
MAEGSSNRITITVKTPKDKKDVEVEEDSTVEKFKVLVAEKFEAEVEQLCLIFAGKIMKDA
DTLKSHNIKDGLTVHLVIKAPPKPEAEGPTRRPADVRQTPFGLNQIGGLSGLEALGANSS
TFMDMQSRMQHELMGNPELMRTILDNPLVQQMLNNPDTMRTLITSNPQMQDLMQRNPEIS
HMLNNPELLRQTMELARNPAMLQELMRSHDRAMSNLESVPGGYNALHRIYRDIQEPMLNA
ASGAFSSNPFSGLVDNGGSENPQQGSENREPLPNPWGGSGNQNSRPAPPPNNILNTPAMQ
SLLQQMGENPEMMSTMMNAPYMRSMMEALSQDPNMAANLISQSPLLQANPQLQDQMRTMM
PQLLQQMQNPEVQNMLSNPDALNAILQIQQGMEQLRQAAPGLVGTMGIPPPPPGTNQPPQ
TGNTPNAPNQQLFNDFMQRMLNGMTNQGTQQNLPPEQRYQSQLEQLSAMGFVNREANLQA
LIATFGDINAAVERLLALGSLSLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g3004.t1 CDD cd01808 Ubl_PLICs 7 79 0.0000000
22 g3004.t1 CDD cd14399 UBA_PLICs 458 494 0.0000000
17 g3004.t1 Gene3D G3DSA:3.10.20.90 - 1 86 0.0000000
18 g3004.t1 Gene3D G3DSA:1.10.260.100 - 168 222 0.0000004
19 g3004.t1 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 442 502 0.0000000
4 g3004.t1 PANTHER PTHR10677 UBIQUILIN 6 88 0.0000000
7 g3004.t1 PANTHER PTHR10677:SF21 UBIQUILIN-4 6 88 0.0000000
3 g3004.t1 PANTHER PTHR10677 UBIQUILIN 103 285 0.0000000
6 g3004.t1 PANTHER PTHR10677:SF21 UBIQUILIN-4 103 285 0.0000000
5 g3004.t1 PANTHER PTHR10677 UBIQUILIN 289 497 0.0000000
8 g3004.t1 PANTHER PTHR10677:SF21 UBIQUILIN-4 289 497 0.0000000
2 g3004.t1 Pfam PF00240 Ubiquitin family 11 80 0.0000000
1 g3004.t1 Pfam PF00627 UBA/TS-N domain 459 495 0.0000001
20 g3004.t1 ProSiteProfiles PS50053 Ubiquitin domain profile. 9 79 17.1040000
21 g3004.t1 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 454 498 11.8720000
12 g3004.t1 SMART SM00213 ubq_7 9 79 0.0000000
14 g3004.t1 SMART SM00727 CBM 136 165 12.0000000
15 g3004.t1 SMART SM00727 CBM 166 205 0.0000000
13 g3004.t1 SMART SM00727 CBM 309 356 0.0000240
16 g3004.t1 SMART SM00727 CBM 360 392 0.6000000
11 g3004.t1 SMART SM00165 uba_6 459 497 0.0000002
9 g3004.t1 SUPERFAMILY SSF54236 Ubiquitin-like 4 86 0.0000000
10 g3004.t1 SUPERFAMILY SSF46934 UBA-like 444 496 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