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.t8 TTS g12937.t8 27009496 27009496
chr_1 g12937 g12937.t8 isoform g12937.t8 27009648 27010699
chr_1 g12937 g12937.t8 exon g12937.t8.exon1 27009648 27009871
chr_1 g12937 g12937.t8 cds g12937.t8.CDS1 27009648 27009871
chr_1 g12937 g12937.t8 exon g12937.t8.exon2 27009934 27009999
chr_1 g12937 g12937.t8 cds g12937.t8.CDS2 27009934 27009999
chr_1 g12937 g12937.t8 exon g12937.t8.exon3 27010180 27010699
chr_1 g12937 g12937.t8 cds g12937.t8.CDS3 27010180 27010663
chr_1 g12937 g12937.t8 TSS g12937.t8 27011325 27011325

Sequences

>g12937.t8 Gene=g12937 Length=810
CTTGTTCTAAAACATCGTCAAGGCAAGAATCATAAAATGCGTATTGTACTTTTTATTGGA
TCACCACTTGAAGTGGATAAAGCTGAAATGGAAAAATTAGCTAAGAAATTGAAGAAAGAA
AAAGTTAATGTCGATATTGTGAGCTTTGGTGACCATCAAAAAAATAATGATGTGCTTACT
TCATTTATTAATACATTGAATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTCCA
AGAGGATCACAATTGCAAGAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATGGA
ATGGGCGCAGGAATTGGTGGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATCCA
GAACTTGCTCTTGCTTTAAGAGTTTCAATGGAAGAACAGCGTCAGCGACAAGAAGAAGAG
CAAAGACGTGCACAAGCAGCTTCTGCTCAAGAAACTTCAACTGAAAATGCTCCAGCTGTT
TCTACTATTGCACCAACATCTGACGAAGCTATGCTTGAACATTTTGCTAACATGACTGAA
GAGGAACAAATTGCTTTTGCTATGCAAATGTCAATGCAAGATGCACAGGAGCCTATAACA
CAACAAGCAAAACGTCCAAAAAAAGACGATACACCAATGGAAGTTGATGAAGATTATAAT
GAAGTAATTACTGATCCAGCATTTCTCCAGAGTGTTTTAGAAAATCTTCCTGGTGTAGAT
CCGCAATCTGAGGCAATACGTGGTGCAGTTGACTCCTTAAATAAAGACAAAAAGTCTGAT
AAAGATGGAAAAGGCAGCGGATCTAAATAA

>g12937.t8 Gene=g12937 Length=257
MRIVLFIGSPLEVDKAEMEKLAKKLKKEKVNVDIVSFGDHQKNNDVLTSFINTLNGKDGT
GSHLVSVPRGSQLQEALISSAIIQGEDGMGAGIGGAGFEFGVDPNEDPELALALRVSMEE
QRQRQEEEQRRAQAASAQETSTENAPAVSTIAPTSDEAMLEHFANMTEEEQIAFAMQMSM
QDAQEPITQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAVDS
LNKDKKSDKDGKGSGSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12937.t8 Coils Coil Coil 11 31 -
15 g12937.t8 Coils Coil Coil 115 138 -
13 g12937.t8 Gene3D G3DSA:3.40.50.410 - 1 80 1.8E-22
14 g12937.t8 Gene3D G3DSA:1.10.10.890 - 149 187 3.3E-9
12 g12937.t8 MobiDBLite mobidb-lite consensus disorder prediction 118 149 -
10 g12937.t8 MobiDBLite mobidb-lite consensus disorder prediction 119 133 -
9 g12937.t8 MobiDBLite mobidb-lite consensus disorder prediction 134 149 -
8 g12937.t8 MobiDBLite mobidb-lite consensus disorder prediction 182 202 -
7 g12937.t8 MobiDBLite mobidb-lite consensus disorder prediction 222 257 -
11 g12937.t8 MobiDBLite mobidb-lite consensus disorder prediction 238 257 -
3 g12937.t8 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 1 252 1.1E-78
4 g12937.t8 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 1 252 1.1E-78
1 g12937.t8 Pfam PF02809 Ubiquitin interaction motif 106 121 0.0064
2 g12937.t8 Pfam PF02809 Ubiquitin interaction motif 167 183 0.0014
18 g12937.t8 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 105 124 10.732
17 g12937.t8 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 167 186 10.363
6 g12937.t8 SMART SM00726 uim 105 124 0.021
5 g12937.t8 SMART SM00726 uim 167 186 0.025

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