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.t7 TTS g12937.t7 27009496 27009496
chr_1 g12937 g12937.t7 isoform g12937.t7 27009648 27010562
chr_1 g12937 g12937.t7 exon g12937.t7.exon1 27009648 27009871
chr_1 g12937 g12937.t7 cds g12937.t7.CDS1 27009648 27009871
chr_1 g12937 g12937.t7 exon g12937.t7.exon2 27009934 27010018
chr_1 g12937 g12937.t7 cds g12937.t7.CDS2 27009934 27010018
chr_1 g12937 g12937.t7 exon g12937.t7.exon3 27010136 27010562
chr_1 g12937 g12937.t7 cds g12937.t7.CDS3 27010136 27010399
chr_1 g12937 g12937.t7 TSS g12937.t7 27011325 27011325

Sequences

>g12937.t7 Gene=g12937 Length=736
TGTGAGCTTTGGTGACCATCAAAAAAATAATGATGTGCTTACTTCATTTATTAATACATT
GAATGGAAAAGATGGTACAGGTTCTCATTTAGTTAGCGTTCCAAGAGGATCACAATTGCA
AGAAGCATTAATTTCATCAGCAATCATTCAAGGAGAAGATGGAATGGGCGCAGGAATTGG
TGGTGCAGGCTTTGAATTTGGTGTTGATCCTAATGAGGATCCAGAACTTGCTCTTGCTTT
AAGAGTTTCAATGGAAGAACAGCGTCAGCGACAAGAAGAAGAGCAAAGACGTGCACAAGC
AGCTTCTGCTCAAGAAACTTCAACTGAAAATGCTCCAGCTGTTTCTACTATTGCACCAAC
ATCTGACGAAGCTATGCTTGAACGTGCACTCGCATTGTCGACTGAGACACCGGTAAAAAG
ACTTCGTAGTGACGAGGCTATGCCAGATTTTGCTAACATGACTGAAGAGGAACAAATTGC
TTTTGCTATGCAAATGTCAATGCAAGATGCACAGGAGCCTATAACACAACAAGCAAAACG
TCCAAAAAAAGACGATACACCAATGGAAGTTGATGAAGATTATAATGAAGTAATTACTGA
TCCAGCATTTCTCCAGAGTGTTTTAGAAAATCTTCCTGGTGTAGATCCGCAATCTGAGGC
AATACGTGGTGCAGTTGACTCCTTAAATAAAGACAAAAAGTCTGATAAAGATGGAAAAGG
CAGCGGATCTAAATAA

>g12937.t7 Gene=g12937 Length=190
MGAGIGGAGFEFGVDPNEDPELALALRVSMEEQRQRQEEEQRRAQAASAQETSTENAPAV
STIAPTSDEAMLERALALSTETPVKRLRSDEAMPDFANMTEEEQIAFAMQMSMQDAQEPI
TQQAKRPKKDDTPMEVDEDYNEVITDPAFLQSVLENLPGVDPQSEAIRGAVDSLNKDKKS
DKDGKGSGSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g12937.t7 Coils Coil Coil 27 50 -
15 g12937.t7 Gene3D G3DSA:1.10.10.890 - 67 114 2.3E-15
13 g12937.t7 MobiDBLite mobidb-lite consensus disorder prediction 30 135 -
9 g12937.t7 MobiDBLite mobidb-lite consensus disorder prediction 31 45 -
14 g12937.t7 MobiDBLite mobidb-lite consensus disorder prediction 46 63 -
12 g12937.t7 MobiDBLite mobidb-lite consensus disorder prediction 105 121 -
11 g12937.t7 MobiDBLite mobidb-lite consensus disorder prediction 155 190 -
10 g12937.t7 MobiDBLite mobidb-lite consensus disorder prediction 171 190 -
4 g12937.t7 PANTHER PTHR10223:SF7 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 4 185 8.5E-43
5 g12937.t7 PANTHER PTHR10223 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4 4 185 8.5E-43
3 g12937.t7 Pfam PF02809 Ubiquitin interaction motif 18 33 0.0044
1 g12937.t7 Pfam PF02809 Ubiquitin interaction motif 67 81 0.013
2 g12937.t7 Pfam PF02809 Ubiquitin interaction motif 100 116 9.2E-4
19 g12937.t7 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 17 36 10.732
18 g12937.t7 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 67 86 8.566
17 g12937.t7 ProSiteProfiles PS50330 Ubiquitin-interacting motif (UIM) domain profile. 100 119 10.363
8 g12937.t7 SMART SM00726 uim 17 36 0.021
7 g12937.t7 SMART SM00726 uim 67 86 4.4
6 g12937.t7 SMART SM00726 uim 100 119 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.

Raw TPM values