Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t4 TTS g12937.t4 27009496 27009496
chr_1 g12937 g12937.t4 isoform g12937.t4 27009648 27010514
chr_1 g12937 g12937.t4 exon g12937.t4.exon1 27009648 27009871
chr_1 g12937 g12937.t4 cds g12937.t4.CDS1 27009648 27009871
chr_1 g12937 g12937.t4 exon g12937.t4.exon2 27009934 27009999
chr_1 g12937 g12937.t4 cds g12937.t4.CDS2 27009934 27009999
chr_1 g12937 g12937.t4 exon g12937.t4.exon3 27010138 27010514
chr_1 g12937 g12937.t4 cds g12937.t4.CDS3 27010138 27010399
chr_1 g12937 g12937.t4 TSS g12937.t4 27011325 27011325

Sequences

>g12937.t4 Gene=g12937 Length=667
TATTAATACATTGAATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGG
ATCACAATTGCAAGAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGG
CGCAGGAATTGGTGGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACT
TGCTCTTGCTTTAAGAGTTTCAATGGAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAG
ACGTGCACAAGCAGCTTCTGCTCAAGAAACTTCAACTGAAAATGCTCCAGCTGTTTCTAC
TATTGCACCAACATCTGACGAAGCTATGCTTGAACGTGCACTCGCATTGTCGACTGAGAC
ACCGGTAAAAAGACTTCATTTTGCTAACATGACTGAAGAGGAACAAATTGCTTTTGCTAT
GCAAATGTCAATGCAAGATGCACAGGAGCCTATAACACAACAAGCAAAACGTCCAAAAAA
AGACGATACACCAATGGAAGTTGATGAAGATTATAATGAAGTAATTACTGATCCAGCATT
TCTCCAGAGTGTTTTAGAAAATCTTCCTGGTGTAGATCCGCAATCTGAGGCAATACGTGG
TGCAGTTGACTCCTTAAATAAAGACAAAAAGTCTGATAAAGATGGAAAAGGCAGCGGATC
TAAATAA

>g12937.t4 Gene=g12937 Length=183
MGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRAQAASAQETSTENAPAV
STIAPTSDEAMLERALALSTETPVKRLHFANMTEEEQIAFAMQMSMQDAQEPITQQAKRP
KKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAVDSLNKDKKSDKDGKGS
GSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12937.t4 Coils Coil Coil 27 50 -
15 g12937.t4 Gene3D G3DSA:1.10.10.890 - 67 107 3.1E-13
10 g12937.t4 MobiDBLite mobidb-lite consensus disorder prediction 29 67 -
9 g12937.t4 MobiDBLite mobidb-lite consensus disorder prediction 31 45 -
14 g12937.t4 MobiDBLite mobidb-lite consensus disorder prediction 46 63 -
11 g12937.t4 MobiDBLite mobidb-lite consensus disorder prediction 108 128 -
13 g12937.t4 MobiDBLite mobidb-lite consensus disorder prediction 148 183 -
12 g12937.t4 MobiDBLite mobidb-lite consensus disorder prediction 164 183 -
4 g12937.t4 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 4 178 4.1E-42
5 g12937.t4 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 4 178 4.1E-42
3 g12937.t4 Pfam PF02809 Ubiquitin interaction motif 18 33 0.0041
2 g12937.t4 Pfam PF02809 Ubiquitin interaction motif 67 81 0.012
1 g12937.t4 Pfam PF02809 Ubiquitin interaction motif 93 109 8.8E-4
18 g12937.t4 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 17 36 10.732
17 g12937.t4 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 67 86 8.566
19 g12937.t4 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 93 112 10.363
7 g12937.t4 SMART SM00726 uim 17 36 0.021
6 g12937.t4 SMART SM00726 uim 67 86 4.4
8 g12937.t4 SMART SM00726 uim 93 112 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