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.t15 TTS g12937.t15 27009496 27009496
chr_1 g12937 g12937.t15 isoform g12937.t15 27009648 27011251
chr_1 g12937 g12937.t15 exon g12937.t15.exon1 27009648 27009871
chr_1 g12937 g12937.t15 cds g12937.t15.CDS1 27009648 27009871
chr_1 g12937 g12937.t15 exon g12937.t15.exon2 27009934 27010018
chr_1 g12937 g12937.t15 cds g12937.t15.CDS2 27009934 27010018
chr_1 g12937 g12937.t15 exon g12937.t15.exon3 27010151 27010699
chr_1 g12937 g12937.t15 cds g12937.t15.CDS3 27010151 27010699
chr_1 g12937 g12937.t15 exon g12937.t15.exon4 27010752 27010858
chr_1 g12937 g12937.t15 cds g12937.t15.CDS4 27010752 27010811
chr_1 g12937 g12937.t15 exon g12937.t15.exon5 27010930 27011070
chr_1 g12937 g12937.t15 exon g12937.t15.exon6 27011226 27011251
chr_1 g12937 g12937.t15 TSS g12937.t15 27011325 27011325

Sequences

>g12937.t15 Gene=g12937 Length=1132
ATGGTTTTAGAAAGTACTATGATTTGCTTGGATAATAGCGATTATCAACGTAATGGAGAT
TATCTACCAACAAGATTGAACGCACAGAAGGATGGTATCAATTTAGTTTGTCTCACAAAA
TTAAGATCGAATCCAGAAAACAATGTTGGTCTTTTAACAATGGCAAAAAGTTTTAGCTAC
TCTGACTAGTGATGTAGGACGAATTATGTCAAAGATGCATCTCGTTCAACCCAACGGAAA
TATTAATTTAGTAACTGGAATTAGAATTGCTCATCTTGTTCTAAAACATCGTCAAGGCAA
GAATCATAAAATGCGTATTGTACTTTTTATTGGATCACCACTTGAAGTGGATAAAGCTGA
AATGGAAAAATTAGCTAAGAAATTGAAGAAAGAAAAAGTTAATGTCGATATTGTGAGCTT
TGGTGACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAATACATTGAATGGAAA
AGATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCAAGAAGCATT
AATTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGGTGGTGCAGG
CTTTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTTAAGAGTTTC
AATGGAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGCAGCTTCTGC
TCAAGAAACTTCAACTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAACATCTGACGA
AGCTATGCTTGAACGTGCACTCGCATTGTCGACTGAGACACCGAGTGACGAGGCTATGCC
AGATTTTGCTAACATGACTGAAGAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCA
AGATGCACAGGAGCCTATAACACAACAAGCAAAACGTCCAAAAAAAGACGATACACCAAT
GGAAGTTGATGAAGATTATAATGAAGTAATTACTGATCCAGCATTTCTCCAGAGTGTTTT
AGAAAATCTTCCTGGTGTAGATCCGCAATCTGAGGCAATACGTGGTGCAGTTGACTCCTT
AAATAAAGACAAAAAGTCTGATAAAGATGGAAAAGGCAGCGGATCTAAATAA

>g12937.t15 Gene=g12937 Length=305
MHLVQPNGNINLVTGIRIAHLVLKHRQGKNHKMRIVLFIGSPLEVDKAEMEKLAKKLKKE
KVNVDIVSFGDHQKNNDVLTSFINTLNGKDGTGSHLVSVPRGSQLQEALISSAIIQGEDG
MGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRAQAASAQETSTENAPAV
STIAPTSDEAMLERALALSTETPSDEAMPDFANMTEEEQIAFAMQMSMQDAQEPITQQAK
RPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAVDSLNKDKKSDKDGK
GSGSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g12937.t15 Coils Coil Coil 43 63 -
9 g12937.t15 Coils Coil Coil 147 170 -
7 g12937.t15 Gene3D G3DSA:3.40.50.410 - 1 112 4.0E-36
8 g12937.t15 Gene3D G3DSA:1.10.10.890 - 187 229 4.8E-17
19 g12937.t15 MobiDBLite mobidb-lite consensus disorder prediction 150 187 -
18 g12937.t15 MobiDBLite mobidb-lite consensus disorder prediction 151 165 -
17 g12937.t15 MobiDBLite mobidb-lite consensus disorder prediction 166 183 -
15 g12937.t15 MobiDBLite mobidb-lite consensus disorder prediction 231 251 -
14 g12937.t15 MobiDBLite mobidb-lite consensus disorder prediction 269 305 -
16 g12937.t15 MobiDBLite mobidb-lite consensus disorder prediction 286 305 -
4 g12937.t15 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 1 300 6.4E-104
5 g12937.t15 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 1 300 6.4E-104
2 g12937.t15 Pfam PF02809 Ubiquitin interaction motif 138 153 0.008
1 g12937.t15 Pfam PF02809 Ubiquitin interaction motif 187 201 0.024
3 g12937.t15 Pfam PF02809 Ubiquitin interaction motif 215 231 0.0017
20 g12937.t15 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 137 156 10.732
21 g12937.t15 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 215 234 10.363
11 g12937.t15 SMART SM00726 uim 137 156 0.021
13 g12937.t15 SMART SM00726 uim 187 206 0.84
12 g12937.t15 SMART SM00726 uim 215 234 0.025
6 g12937.t15 SUPERFAMILY SSF53300 vWA-like 2 103 2.4E-13

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