Gene loci information

Transcript annotation

  • This transcript has been annotated as 26S proteasome non-ATPase regulatory subunit 4.

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_1 g12937 g12937.t31 TTS g12937.t31 27009496 27009496
chr_1 g12937 g12937.t31 isoform g12937.t31 27010151 27011077
chr_1 g12937 g12937.t31 exon g12937.t31.exon1 27010151 27010699
chr_1 g12937 g12937.t31 cds g12937.t31.CDS1 27010151 27010699
chr_1 g12937 g12937.t31 exon g12937.t31.exon2 27010752 27010866
chr_1 g12937 g12937.t31 cds g12937.t31.CDS2 27010752 27010866
chr_1 g12937 g12937.t31 exon g12937.t31.exon3 27010930 27011077
chr_1 g12937 g12937.t31 cds g12937.t31.CDS3 27010930 27010937
chr_1 g12937 g12937.t31 TSS g12937.t31 27011325 27011325

Sequences

>g12937.t31 Gene=g12937 Length=812
ATTTTAGCTTGGATAATAGCGATTATCAACGTAATGGAGATTATCTACCAACAAGATTGA
ACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAATTAAGATCGAATCCAGAAA
ACAATGTTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTTTTAGCTACTCTGACTAGTG
ATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCCAACGGAAATATTAATTTAG
TAACTGGAATTAGAATTGCTCATCTTGTTCTAAAACATCGTCAAGGCAAGAATCATAAAA
TGCGTATTGTACTTTTTATTGGATCACCACTTGAAGTGGATAAAGCTGAAATGGAAAAAT
TAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATTGTGAGCTTTGGTGACCATC
AAAAAAATAATGATGTGCTTACTTCATTTATTAATACATTGAATGGAAAAGATGGTACAG
GTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAAGAAGCATTAATTTCATCAG
CAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGTGGTGCAGGCTTTGAATTTG
GTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTAAGAGTTTCAATGGAAGAAC
AGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCAGCTTCTGCTCAAGAAACTT
CAACTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAACATCTGACGAAGCTATGCTTG
AACGTGCACTCGCATTGTCGACTGAGACACCG

>g12937.t31 Gene=g12937 Length=224
MAKTVEVLATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFI
GSPLEVDKAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSV
PRGSQLQEALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEE
EQRRAQAASAQETSTENAPAVSTIAPTSDEAMLERALALSTETP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g12937.t31 Coils Coil Coil 64 84 -
9 g12937.t31 Coils Coil Coil 168 191 -
7 g12937.t31 Gene3D G3DSA:3.40.50.410 - 1 133 2.8E-44
13 g12937.t31 MobiDBLite mobidb-lite consensus disorder prediction 172 224 -
14 g12937.t31 MobiDBLite mobidb-lite consensus disorder prediction 172 186 -
12 g12937.t31 MobiDBLite mobidb-lite consensus disorder prediction 187 204 -
4 g12937.t31 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 2 214 1.8E-86
5 g12937.t31 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 2 214 1.8E-86
1 g12937.t31 Pfam PF13519 von Willebrand factor type A domain 1 60 1.5E-7
2 g12937.t31 Pfam PF02809 Ubiquitin interaction motif 159 174 0.0054
3 g12937.t31 Pfam PF02809 Ubiquitin interaction motif 208 222 0.016
15 g12937.t31 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 158 177 10.732
11 g12937.t31 SMART SM00726 uim 158 177 0.021
10 g12937.t31 SMART SM00726 uim 208 224 570.0
6 g12937.t31 SUPERFAMILY SSF53300 vWA-like 3 124 2.4E-17

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed