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.t15 TTS g1602.t15 12086105 12086105
chr_3 g1602 g1602.t15 isoform g1602.t15 12086814 12087914
chr_3 g1602 g1602.t15 exon g1602.t15.exon1 12086814 12086869
chr_3 g1602 g1602.t15 cds g1602.t15.CDS1 12086815 12086869
chr_3 g1602 g1602.t15 exon g1602.t15.exon2 12086934 12087171
chr_3 g1602 g1602.t15 cds g1602.t15.CDS2 12086934 12087171
chr_3 g1602 g1602.t15 exon g1602.t15.exon3 12087358 12087784
chr_3 g1602 g1602.t15 cds g1602.t15.CDS3 12087358 12087784
chr_3 g1602 g1602.t15 exon g1602.t15.exon4 12087912 12087914
chr_3 g1602 g1602.t15 cds g1602.t15.CDS4 12087912 12087914
chr_3 g1602 g1602.t15 TSS g1602.t15 12088004 12088004

Sequences

>g1602.t15 Gene=g1602 Length=724
ATGGGCCAAAATCAATCTTCTGGTAGTGGAGATAAAAAAGATGATAAAGACAAGAAGAAG
AAGTACGAGCCACCAATTCCAACTCGCGTTGGTAAAAAGAAGCGAAAACAGAAGGGACCA
GATGCTGCATTAAAACTTCCGCAAGTCACTCCGCATACTCGTTGTCGTTTGAAATTGCTT
AAACTTGAACGCATCAAAGATTACCTTCTTATGGAAGAGGAATTTATTCGTAATCAAGAG
CGTTTGAAGCCTCAAGAAGAGAAGAATGAAGAAGAAAGGTCGAAAGTTGATGATTTGAGA
GGAACACCAATGTCTGTTGGTAATCTGGAAGAAATCATTGATGATAATCATGCAATTGTT
TCAACATCAGTTGGTAGTGAGCATTACGTTAGCATATTATCATTTGTCGATAAAGATCAA
CTTGAACCAGGATGTTCGGTCTTATTAAATCATAAAGTTCATGCTGTAGTTGGTGTATTA
AGTGATGATACAGATCCAATGGTTACGGTAATGAAATTAGAAAAAGCTCCACAAGAAACT
TATGCCGATATTGGCGGATTAGATACGCAAATTCAAGAAATTAAAGAGTCTGTTGAATTA
CCTTTAACACATCCTGAATATTATGAAGAAATGGGTATTAAACCACCAAAAGGAGTCATT
TTATATGGTCCACCAGGTACAGGCAAAACTTTACTTGCTAAAGCTGTAGCTAATCAGACA
TCAG

>g1602.t15 Gene=g1602 Length=241
MGQNQSSGSGDKKDDKDKKKKYEPPIPTRVGKKKRKQKGPDAALKLPQVTPHTRCRLKLL
KLERIKDYLLMEEEFIRNQERLKPQEEKNEEERSKVDDLRGTPMSVGNLEEIIDDNHAIV
STSVGSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVVGVLSDDTDPMVTVMKLEKAPQET
YADIGGLDTQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQT
S

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1602.t15 CDD cd00009 AAA 185 239 2.99348E-9
9 g1602.t15 Gene3D G3DSA:2.40.50.140 - 104 171 2.2E-29
8 g1602.t15 Gene3D G3DSA:3.40.50.300 - 172 241 1.5E-23
6 g1602.t15 MobiDBLite mobidb-lite consensus disorder prediction 1 48 -
7 g1602.t15 MobiDBLite mobidb-lite consensus disorder prediction 9 30 -
3 g1602.t15 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 28 241 8.5E-126
4 g1602.t15 PANTHER PTHR23073:SF77 26S PROTEASOME REGULATORY SUBUNIT 4 28 241 8.5E-126
1 g1602.t15 Pfam PF16450 Proteasomal ATPase OB C-terminal domain 106 160 1.9E-11
2 g1602.t15 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 219 240 6.6E-7
5 g1602.t15 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 165 239 9.44E-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:0036402 proteasome-activating activity 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