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.t1 TTS g12937.t1 27009496 27009496
chr_1 g12937 g12937.t1 isoform g12937.t1 27009648 27011251
chr_1 g12937 g12937.t1 exon g12937.t1.exon1 27009648 27009871
chr_1 g12937 g12937.t1 cds g12937.t1.CDS1 27009648 27009871
chr_1 g12937 g12937.t1 exon g12937.t1.exon2 27009934 27010018
chr_1 g12937 g12937.t1 cds g12937.t1.CDS2 27009934 27010018
chr_1 g12937 g12937.t1 exon g12937.t1.exon3 27010151 27010699
chr_1 g12937 g12937.t1 cds g12937.t1.CDS3 27010151 27010699
chr_1 g12937 g12937.t1 exon g12937.t1.exon4 27010752 27010866
chr_1 g12937 g12937.t1 cds g12937.t1.CDS4 27010752 27010866
chr_1 g12937 g12937.t1 exon g12937.t1.exon5 27010930 27011070
chr_1 g12937 g12937.t1 cds g12937.t1.CDS5 27010930 27011070
chr_1 g12937 g12937.t1 exon g12937.t1.exon6 27011226 27011251
chr_1 g12937 g12937.t1 cds g12937.t1.CDS6 27011226 27011251
chr_1 g12937 g12937.t1 TSS g12937.t1 27011325 27011325

Sequences

>g12937.t1 Gene=g12937 Length=1140
ATGGTTTTAGAAAGTACTATGATTTGCTTGGATAATAGCGATTATCAACGTAATGGAGAT
TATCTACCAACAAGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAA
TTAAGATCGAATCCAGAAAACAATGTTGGTCTTTTAACAATGGCAAAAACTGTAGAAGTT
TTAGCTACTCTGACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCC
AACGGAAATATTAATTTAGTAACTGGAATTAGAATTGCTCATCTTGTTCTAAAACATCGT
CAAGGCAAGAATCATAAAATGCGTATTGTACTTTTTATTGGATCACCACTTGAAGTGGAT
AAAGCTGAAATGGAAAAATTAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATT
GTGAGCTTTGGTGACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAATACATTG
AATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAA
GAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGT
GGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTA
AGAGTTTCAATGGAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCA
GCTTCTGCTCAAGAAACTTCAACTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAACA
TCTGACGAAGCTATGCTTGAACGTGCACTCGCATTGTCGACTGAGACACCGAGTGACGAG
GCTATGCCAGATTTTGCTAACATGACTGAAGAGGAACAAATTGCTTTTGCTATGCAAATG
TCAATGCAAGATGCACAGGAGCCTATAACACAACAAGCAAAACGTCCAAAAAAAGACGAT
ACACCAATGGAAGTTGATGAAGATTATAATGAAGTAATTACTGATCCAGCATTTCTCCAG
AGTGTTTTAGAAAATCTTCCTGGTGTAGATCCGCAATCTGAGGCAATACGTGGTGCAGTT
GACTCCTTAAATAAAGACAAAAAGTCTGATAAAGATGGAAAAGGCAGCGGATCTAAATAA

>g12937.t1 Gene=g12937 Length=379
MVLESTMICLDNSDYQRNGDYLPTRLNAQKDGINLVCLTKLRSNPENNVGLLTMAKTVEV
LATLTSDVGRIMSKMHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFIGSPLEVD
KAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSVPRGSQLQ
EALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRAQA
ASAQETSTENAPAVSTIAPTSDEAMLERALALSTETPSDEAMPDFANMTEEEQIAFAMQM
SMQDAQEPITQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAV
DSLNKDKKSDKDGKGSGSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12937.t1 Coils Coil Coil 117 137 -
10 g12937.t1 Coils Coil Coil 221 244 -
8 g12937.t1 Gene3D G3DSA:3.40.50.410 - 3 186 1.0E-69
9 g12937.t1 Gene3D G3DSA:1.10.10.890 - 261 303 6.5E-17
17 g12937.t1 MobiDBLite mobidb-lite consensus disorder prediction 224 261 -
19 g12937.t1 MobiDBLite mobidb-lite consensus disorder prediction 225 239 -
18 g12937.t1 MobiDBLite mobidb-lite consensus disorder prediction 240 257 -
16 g12937.t1 MobiDBLite mobidb-lite consensus disorder prediction 305 325 -
21 g12937.t1 MobiDBLite mobidb-lite consensus disorder prediction 343 379 -
20 g12937.t1 MobiDBLite mobidb-lite consensus disorder prediction 360 379 -
5 g12937.t1 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 9 374 8.1E-137
6 g12937.t1 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 9 374 8.1E-137
1 g12937.t1 Pfam PF13519 von Willebrand factor type A domain 6 113 2.2E-21
3 g12937.t1 Pfam PF02809 Ubiquitin interaction motif 212 227 0.01
2 g12937.t1 Pfam PF02809 Ubiquitin interaction motif 261 275 0.031
4 g12937.t1 Pfam PF02809 Ubiquitin interaction motif 289 305 0.0022
22 g12937.t1 ProSiteProfiles PS50234 VWFA domain profile. 5 188 9.725
24 g12937.t1 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 211 230 10.732
23 g12937.t1 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 289 308 10.363
15 g12937.t1 SMART SM00327 VWA_4 2 188 1.8E-4
14 g12937.t1 SMART SM00726 uim 211 230 0.021
13 g12937.t1 SMART SM00726 uim 261 280 0.84
12 g12937.t1 SMART SM00726 uim 289 308 0.025
7 g12937.t1 SUPERFAMILY SSF53300 vWA-like 4 177 1.3E-30

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

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