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.t9 TTS g12937.t9 27009496 27009496
chr_1 g12937 g12937.t9 isoform g12937.t9 27009648 27011071
chr_1 g12937 g12937.t9 exon g12937.t9.exon1 27009648 27009871
chr_1 g12937 g12937.t9 cds g12937.t9.CDS1 27009648 27009871
chr_1 g12937 g12937.t9 exon g12937.t9.exon2 27009934 27010018
chr_1 g12937 g12937.t9 cds g12937.t9.CDS2 27009934 27010018
chr_1 g12937 g12937.t9 exon g12937.t9.exon3 27010151 27010699
chr_1 g12937 g12937.t9 cds g12937.t9.CDS3 27010151 27010699
chr_1 g12937 g12937.t9 exon g12937.t9.exon4 27010752 27010866
chr_1 g12937 g12937.t9 cds g12937.t9.CDS4 27010752 27010866
chr_1 g12937 g12937.t9 exon g12937.t9.exon5 27010930 27011071
chr_1 g12937 g12937.t9 cds g12937.t9.CDS5 27010930 27010937
chr_1 g12937 g12937.t9 TSS g12937.t9 27011325 27011325

Sequences

>g12937.t9 Gene=g12937 Length=1115
GCTTGGATAATAGCGATTATCAACGTAATGGAGATTATCTACCAACAAGATTGAACGCAC
AGAAGGATGGTATCAATTTAGTTTGTCTCACAAAATTAAGATCGAATCCAGAAAACAATG
TTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTTTTAGCTACTCTGACTAGTGATGTAG
GACGAATTATGTCAAAGATGCATCTCGTTCAACCCAACGGAAATATTAATTTAGTAACTG
GAATTAGAATTGCTCATCTTGTTCTAAAACATCGTCAAGGCAAGAATCATAAAATGCGTA
TTGTACTTTTTATTGGATCACCACTTGAAGTGGATAAAGCTGAAATGGAAAAATTAGCTA
AGAAATTGAAGAAAGAAAAAGTTAATGTCGATATTGTGAGCTTTGGTGACCATCAAAAAA
ATAATGATGTGCTTACTTCATTTATTAATACATTGAATGGAAAAGATGGTACAGGTTCTC
ATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAAGAAGCATTAATTTCATCAGCAATCA
TTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGTGGTGCAGGCTTTGAATTTGGTGTTG
ATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTAAGAGTTTCAATGGAAGAACAGCGTC
AGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCAGCTTCTGCTCAAGAAACTTCAACTG
AAAATGCTCCAGCTGTTTCTACTATTGCACCAACATCTGACGAAGCTATGCTTGAACGTG
CACTCGCATTGTCGACTGAGACACCGAGTGACGAGGCTATGCCAGATTTTGCTAACATGA
CTGAAGAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCAAGATGCACAGGAGCCTA
TAACACAACAAGCAAAACGTCCAAAAAAAGACGATACACCAATGGAAGTTGATGAAGATT
ATAATGAAGTAATTACTGATCCAGCATTTCTCCAGAGTGTTTTAGAAAATCTTCCTGGTG
TAGATCCGCAATCTGAGGCAATACGTGGTGCAGTTGACTCCTTAAATAAAGACAAAAAGT
CTGATAAAGATGGAAAAGGCAGCGGATCTAAATAA

>g12937.t9 Gene=g12937 Length=326
MAKTVEVLATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFI
GSPLEVDKAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSV
PRGSQLQEALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEE
EQRRAQAASAQETSTENAPAVSTIAPTSDEAMLERALALSTETPSDEAMPDFANMTEEEQ
IAFAMQMSMQDAQEPITQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQS
EAIRGAVDSLNKDKKSDKDGKGSGSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12937.t9 Coils Coil Coil 64 84 -
11 g12937.t9 Coils Coil Coil 168 191 -
8 g12937.t9 Gene3D G3DSA:3.40.50.410 - 1 133 7.0E-44
9 g12937.t9 Gene3D G3DSA:1.10.10.890 - 208 250 5.2E-17
19 g12937.t9 MobiDBLite mobidb-lite consensus disorder prediction 171 208 -
18 g12937.t9 MobiDBLite mobidb-lite consensus disorder prediction 172 186 -
17 g12937.t9 MobiDBLite mobidb-lite consensus disorder prediction 187 204 -
15 g12937.t9 MobiDBLite mobidb-lite consensus disorder prediction 252 272 -
20 g12937.t9 MobiDBLite mobidb-lite consensus disorder prediction 290 326 -
16 g12937.t9 MobiDBLite mobidb-lite consensus disorder prediction 307 326 -
5 g12937.t9 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 2 321 2.9E-113
6 g12937.t9 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 2 321 2.9E-113
1 g12937.t9 Pfam PF13519 von Willebrand factor type A domain 1 60 2.9E-7
2 g12937.t9 Pfam PF02809 Ubiquitin interaction motif 159 174 0.0087
3 g12937.t9 Pfam PF02809 Ubiquitin interaction motif 208 222 0.026
4 g12937.t9 Pfam PF02809 Ubiquitin interaction motif 236 252 0.0018
21 g12937.t9 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 158 177 10.732
22 g12937.t9 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 236 255 10.363
13 g12937.t9 SMART SM00726 uim 158 177 0.021
12 g12937.t9 SMART SM00726 uim 208 227 0.84
14 g12937.t9 SMART SM00726 uim 236 255 0.025
7 g12937.t9 SUPERFAMILY SSF53300 vWA-like 3 124 6.16E-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.

Raw TPM values