Gene loci information

Transcript annotation

  • This transcript has been annotated as 26S proteasome regulatory subunit 10B.

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_2 g6491 g6491.t7 TTS g6491.t7 17249251 17249251
chr_2 g6491 g6491.t7 isoform g6491.t7 17249986 17250741
chr_2 g6491 g6491.t7 exon g6491.t7.exon1 17249986 17250029
chr_2 g6491 g6491.t7 cds g6491.t7.CDS1 17249988 17250029
chr_2 g6491 g6491.t7 exon g6491.t7.exon2 17250083 17250402
chr_2 g6491 g6491.t7 cds g6491.t7.CDS2 17250083 17250402
chr_2 g6491 g6491.t7 exon g6491.t7.exon3 17250461 17250580
chr_2 g6491 g6491.t7 cds g6491.t7.CDS3 17250461 17250580
chr_2 g6491 g6491.t7 exon g6491.t7.exon4 17250645 17250741
chr_2 g6491 g6491.t7 cds g6491.t7.CDS4 17250645 17250741
chr_2 g6491 g6491.t7 TSS g6491.t7 17250826 17250826

Sequences

>g6491.t7 Gene=g6491 Length=581
ATGACTACTGTAGCTGATCCAGTTCGCGAAAAGGCATTACAGGACTATCGAAAGAAATTA
TTGGAGCATAAGGAAGTCGAGTCTCGTTTGAAAGAAATTCGCGAGTCACTTAAAGATAGC
ACAAAGCAATTTGATAAGTCTGAAAATGATTTGAAAGCACTACAAAGTGTTGGTCAAATT
GTAGGTGAAGTTTTAAAGCAGCTTACCGAAGATAAATTCATTGTTAAAGCTACAAATGGT
CCACGTTATGTTGTTGGTTGTAGACGTCAATTGGACAAGTCAAAATTAAAATCAGGAACA
AGAGTTGCTTTAGATATGACAACACTCACTATTATGCGTTATTTACCACGAGAAGTTGAT
CCTCTCGTGTACAATATGTCGCATGAAGATCCAGGCGATGTCACTTATTCTGCTATTGGT
GGTCTCTCTGAACAAATTCGAGAATTAAGAGAAGTCATTGAACTTCCTTTATTAAATCCA
GAGTTATTTTTAAGAGTTGGTATCACTCCACCAAAGGGATGTCTTCTTTATGGACCACCT
GGTACAGGAAAAACTTTATTAGCTCGTGCTGTAGCATCACA

>g6491.t7 Gene=g6491 Length=193
MTTVADPVREKALQDYRKKLLEHKEVESRLKEIRESLKDSTKQFDKSENDLKALQSVGQI
VGEVLKQLTEDKFIVKATNGPRYVVGCRRQLDKSKLKSGTRVALDMTTLTIMRYLPREVD
PLVYNMSHEDPGDVTYSAIGGLSEQIRELREVIELPLLNPELFLRVGITPPKGCLLYGPP
GTGKTLLARAVAS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6491.t7 CDD cd00009 AAA 140 192 5.04397E-9
8 g6491.t7 Coils Coil Coil 23 57 -
7 g6491.t7 Gene3D G3DSA:2.40.50.140 - 22 126 6.8E-35
6 g6491.t7 Gene3D G3DSA:3.40.50.300 - 127 193 1.2E-20
3 g6491.t7 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 3 193 1.2E-98
4 g6491.t7 PANTHER PTHR23073:SF76 26S PROTEASOME REGULATORY SUBUNIT 10B 3 193 1.2E-98
1 g6491.t7 Pfam PF16450 Proteasomal ATPase OB C-terminal domain 61 116 6.0E-10
2 g6491.t7 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 175 192 5.9E-6
5 g6491.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 64 192 5.14E-21

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005524 ATP binding MF
GO:0030433 ubiquitin-dependent ERAD pathway BP
GO:0016887 ATP hydrolysis activity MF
GO:0008540 proteasome regulatory particle, base subcomplex CC

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