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.t5 TSS g3004.t5 21915593 21915593
chr_3 g3004 g3004.t5 isoform g3004.t5 21915821 21918043
chr_3 g3004 g3004.t5 exon g3004.t5.exon1 21915821 21915916
chr_3 g3004 g3004.t5 cds g3004.t5.CDS1 21915821 21915916
chr_3 g3004 g3004.t5 exon g3004.t5.exon2 21916198 21916329
chr_3 g3004 g3004.t5 cds g3004.t5.CDS2 21916198 21916329
chr_3 g3004 g3004.t5 exon g3004.t5.exon3 21916390 21917293
chr_3 g3004 g3004.t5 cds g3004.t5.CDS3 21916390 21917293
chr_3 g3004 g3004.t5 exon g3004.t5.exon4 21917363 21917599
chr_3 g3004 g3004.t5 cds g3004.t5.CDS4 21917363 21917599
chr_3 g3004 g3004.t5 exon g3004.t5.exon5 21917663 21918043
chr_3 g3004 g3004.t5 cds g3004.t5.CDS5 21917663 21917739
chr_3 g3004 g3004.t5 TTS g3004.t5 21918308 21918308

Sequences

>g3004.t5 Gene=g3004 Length=1750
ATGGCAGAAGGATCATCAAATCGTATTACGATAACAGTAAAAACACCTAAGGATAAGAAA
GATGTTGAAGTTGAAGAAGATTCTACAGTAGAGAAGTTCAAAGTTCTTGTTGCTGAAAAG
TTTGAAGCTGAAGTTGAGCAATTGTGCTTGATTTTTGCTGGAAAAATTATGAAAGATGCA
GACACTCTTAAAAGTCACAATATAAAAGACGGATTGACAGTTCATTTGGTTATCAAAGCT
CCACCAAAACCTGAAGCAGAAGGTCCAACACGACGACCAGCAGACGTACGTCAAACACCA
TTCGGTTTAAATCAAATTGGTGGTCTATCAGGACTTGAAGCGCTCGGTGCTAATTCAAGT
ACATTCATGGATATGCAATCTCGAATGCAGCATGAATTGATGGGGAATCCTGAGTTAATG
AGAACAATTTTAGATAACCCCTTAGTTCAACAAATGCTTAATAATCCAGACACAATGAGA
ACCTTAATTACGAGCAATCCTCAAATGCAAGATTTAATGCAGCGTAATCCAGAAATTTCT
CACATGCTCAATAATCCCGAATTGTTGCGACAAACTATGGAACTTGCAAGGAATCCAGCT
ATGTTGCAAGAGTTGATGCGTTCACACGATAGAGCAATGTCTAATTTGGAATCAGTTCCA
GGTGGTTATAATGCGCTACATCGCATTTATCGTGATATTCAAGAGCCAATGCTGAATGCA
GCTTCTGGAGCATTTTCATCAAACCCATTCAGTGGATTAGTTGATAATGGAGGTTCTGAG
AATCCTCAACAAGGAAGTGAAAATCGTGAACCATTACCAAATCCATGGGGCGGTAGTGGA
AATCAAAATTCCCGACCAGCTCCACCACCAAATAATATTTTAAACACTCCAGCAATGCAA
AGTCTTTTACAACAAATGGGAGAAAATCCTGAAATGATGTCAACTATGATGAATGCACCA
TATATGCGTTCAATGATGGAAGCACTTTCACAAGATCCGAATATGGCGGCAAATTTGATT
AGTCAAAGTCCTCTTCTTCAAGCAAATCCACAATTGCAAGATCAAATGAGAACAATGATG
CCGCAACTTTTACAGCAAATGCAAAATCCAGAAGTTCAAAATATGCTGTCCAGATTAGTT
GGAACCATGGGAATTCCACCACCTCCTCCCGGAACGAATCAGCCACCACAAACTGGAAAC
ACACCGAATGCACCAAATCAACAACTTTTTAATGACTTTATGCAACGAATGCTTAATGGA
ATGACCAATCAAGGAACACAACAGAATTTACCACCAGAACAGCGATATCAGTCGCAACTT
GAGCAGCTTTCAGCTATGGGATTTGTAAATCGTGAAGCCAATTTACAAGCATTAATCGCG
ACATTCGGAGACATAAATGCAGCAGTTGAACGATTGTTGGCATTGGGATCATTGTCATTA
AGTTAACTTAATTAAATGGACGGTAAGATAAAGGAAGCAAAAGAATTAGAGTGGATGATA
TAAAAAATTTACCCTTTCCCAATCAACACAATATATATATATATATATACACATTTATTT
CTATTGATCTTCTCATTCTCTTCAGTTATTCAAATAAGTTTATTTTATGAAAAAAAAAAA
TACATTTCAAAATTTTCCTTTCTTATAATTTTTTCTTTTCTATAAATAATTATTTAGAAT
ATGAGACATTATTGCTAAATTTATATGATATGTAAATTAAAAAATGGGGAAAAAATATTT
GGAGTTGAAA

>g3004.t5 Gene=g3004 Length=481
MAEGSSNRITITVKTPKDKKDVEVEEDSTVEKFKVLVAEKFEAEVEQLCLIFAGKIMKDA
DTLKSHNIKDGLTVHLVIKAPPKPEAEGPTRRPADVRQTPFGLNQIGGLSGLEALGANSS
TFMDMQSRMQHELMGNPELMRTILDNPLVQQMLNNPDTMRTLITSNPQMQDLMQRNPEIS
HMLNNPELLRQTMELARNPAMLQELMRSHDRAMSNLESVPGGYNALHRIYRDIQEPMLNA
ASGAFSSNPFSGLVDNGGSENPQQGSENREPLPNPWGGSGNQNSRPAPPPNNILNTPAMQ
SLLQQMGENPEMMSTMMNAPYMRSMMEALSQDPNMAANLISQSPLLQANPQLQDQMRTMM
PQLLQQMQNPEVQNMLSRLVGTMGIPPPPPGTNQPPQTGNTPNAPNQQLFNDFMQRMLNG
MTNQGTQQNLPPEQRYQSQLEQLSAMGFVNREANLQALIATFGDINAAVERLLALGSLSL
S

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g3004.t5 CDD cd01808 Ubl_PLICs 7 79 0.0000000
23 g3004.t5 CDD cd14399 UBA_PLICs 435 471 0.0000000
18 g3004.t5 Gene3D G3DSA:3.10.20.90 - 1 86 0.0000000
19 g3004.t5 Gene3D G3DSA:1.10.260.100 - 168 222 0.0000003
20 g3004.t5 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 419 479 0.0000000
5 g3004.t5 PANTHER PTHR10677 UBIQUILIN 6 88 0.0000000
9 g3004.t5 PANTHER PTHR10677:SF21 UBIQUILIN-4 6 88 0.0000000
3 g3004.t5 PANTHER PTHR10677 UBIQUILIN 103 285 0.0000000
7 g3004.t5 PANTHER PTHR10677:SF21 UBIQUILIN-4 103 285 0.0000000
6 g3004.t5 PANTHER PTHR10677 UBIQUILIN 289 376 0.0000000
10 g3004.t5 PANTHER PTHR10677:SF21 UBIQUILIN-4 289 376 0.0000000
4 g3004.t5 PANTHER PTHR10677 UBIQUILIN 384 474 0.0000000
8 g3004.t5 PANTHER PTHR10677:SF21 UBIQUILIN-4 384 474 0.0000000
2 g3004.t5 Pfam PF00240 Ubiquitin family 11 80 0.0000000
1 g3004.t5 Pfam PF00627 UBA/TS-N domain 436 472 0.0000000
21 g3004.t5 ProSiteProfiles PS50053 Ubiquitin domain profile. 9 79 17.1040000
22 g3004.t5 ProSiteProfiles PS50030 Ubiquitin-associated domain (UBA) profile. 431 475 11.8720000
14 g3004.t5 SMART SM00213 ubq_7 9 79 0.0000000
16 g3004.t5 SMART SM00727 CBM 136 165 12.0000000
17 g3004.t5 SMART SM00727 CBM 166 205 0.0000000
15 g3004.t5 SMART SM00727 CBM 309 356 0.0000240
13 g3004.t5 SMART SM00165 uba_6 436 474 0.0000002
11 g3004.t5 SUPERFAMILY SSF54236 Ubiquitin-like 4 86 0.0000000
12 g3004.t5 SUPERFAMILY SSF46934 UBA-like 421 473 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