Gene loci information

Transcript annotation

  • This transcript has been annotated as 26S proteasome 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_3 g1602 g1602.t7 TTS g1602.t7 12086105 12086105
chr_3 g1602 g1602.t7 isoform g1602.t7 12086169 12087171
chr_3 g1602 g1602.t7 exon g1602.t7.exon1 12086169 12086711
chr_3 g1602 g1602.t7 cds g1602.t7.CDS1 12086169 12086567
chr_3 g1602 g1602.t7 exon g1602.t7.exon2 12086774 12086861
chr_3 g1602 g1602.t7 exon g1602.t7.exon3 12086934 12087171
chr_3 g1602 g1602.t7 TSS g1602.t7 12088004 12088004

Sequences

>g1602.t7 Gene=g1602 Length=869
GATGTTCGGTCTTATTAAATCATAAAGTTCATGCTGTAGTTGGTGTATTAAGTGATGATA
CAGATCCAATGGTTACGGTAATGAAATTAGAAAAAGCTCCACAAGAAACTTATGCCGATA
TTGGCGGATTAGATACGCAAATTCAAGAAATTAAAGAGTCTGTTGAATTACCTTTAACAC
ATCCTGAATATTATGAAGAAATGGGTATTAAACCACCAAAAGGAGTCATTTTATATGGGT
ACAGGCAAAACTTTACTTGCTAAAGCTGTAGCTAATCAGACATCAGCTACTTTCCTACGT
GTTGTTGGATCAGAATTAATTCAAAAGGTGATGGTCCAAAATTAGTTCGTGAATTGTTTC
GCGTTGCAGAAGAACACGCACCATCTATCGTTTTTATTGATGAAATTGATGCAGTTGGCA
CAAAACGTTATGATTCAAATTCAGGCGGTGAGAGAGAAATTCAAAGAACTATGTTGGAGT
TGCTTAATCAATTAGATGGTTTTGATTCACGTGGTGATGTGAAAGTTATTATGGCAACAA
ATAGAATTGAAACTCTTGATCCTGCTCTCATTCGTCCCGGACGTATTGATCGTAAAATTG
AATTCCCTCTGCCAGATGAGAAGACAAAGAGAAGAATTTTCAATATTCACACTTCAAAAA
TGACACTCGCATCCGATGTCAATCTTTCTGAATTAATTATGGCAAAAGATGATTTGTCTG
GGGCTGATATAAAAGCTATTTGTACTGAAGCTGGTTTGATGGCTTTGCGTGAACGTCGAA
TGAAGGTTACAAATGATGACTTTAAGAAATCGAAAGAGAGTGTACTTTATCGTAAAAAAG
AAGGAACCCCAGATGGTTTATATTTGTAA

>g1602.t7 Gene=g1602 Length=132
MLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIH
TSKMTLASDVNLSELIMAKDDLSGADIKAICTEAGLMALRERRMKVTNDDFKKSKESVLY
RKKEGTPDGLYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g1602.t7 CDD cd00009 AAA 1 47 2.7075E-4
7 g1602.t7 Gene3D G3DSA:3.40.50.300 - 1 48 1.5E-15
8 g1602.t7 Gene3D G3DSA:1.10.8.60 - 52 128 6.0E-23
3 g1602.t7 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 2 131 4.7E-75
4 g1602.t7 PANTHER PTHR23073:SF79 - 2 131 4.7E-75
1 g1602.t7 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 3 47 9.1E-10
2 g1602.t7 Pfam PF17862 AAA+ lid domain 69 113 9.3E-12
6 g1602.t7 ProSitePatterns PS00674 AAA-protein family signature. 17 35 -
5 g1602.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 125 1.1E-25

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:0016887 ATP hydrolysis activity MF

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