Gene loci information

Transcript annotation

  • This transcript has been annotated as Proteasome subunit alpha type-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 g4076 g4076.t9 TSS g4076.t9 30464628 30464628
chr_3 g4076 g4076.t9 isoform g4076.t9 30464746 30465808
chr_3 g4076 g4076.t9 exon g4076.t9.exon1 30464746 30464748
chr_3 g4076 g4076.t9 cds g4076.t9.CDS1 30464746 30464748
chr_3 g4076 g4076.t9 exon g4076.t9.exon2 30464874 30465327
chr_3 g4076 g4076.t9 cds g4076.t9.CDS2 30464874 30465327
chr_3 g4076 g4076.t9 exon g4076.t9.exon3 30465454 30465808
chr_3 g4076 g4076.t9 cds g4076.t9.CDS3 30465454 30465467
chr_3 g4076 g4076.t9 TTS g4076.t9 30465804 30465804

Sequences

>g4076.t9 Gene=g4076 Length=812
ATGGCACGCAGATATGATTCAAGAACCACTATCTTTTCACCAGAAGGTCGTTTGTATCAA
GTAGAATATGCTATGGAGGCAATTTCGCATGCTGGTACTTGCTTAGGAATTTTAGCAAAA
GACGGAATTCTGTTGGCAGCTGAACGCCGAAATATTAATAAACTTCTCGATAATAGCATC
TTTGCTGAAAAGATTTACAGATTAAATGAAGATATGGTCTGCAGCGTTGCTGGAATTACA
TCTGATGCAAACGTTCTCACAAATGAGTTACGTTTAATTGCACAACGATATCAATTACAG
TATGATGAGCCAATTCCAGTTGAACAATTGGTTTCAAGCTTATGTGATCTAAAGCAAGCA
TACACACAATATGGTGGTAAACGTCCGTTTGGAGTATCGATTCTTTACATGGGTTGGGAT
AAGCACTATGGATATCAATTGTATCAATCAGATCCAACAAGAATTAAATGAAACTCCGAT
TTCGCTTGCAGAAGCCGAAGATATGGCAATTAAAGTTCTCTCAAAAACTCTAGACATGAC
TAAATTGACATCAGAGAAAATTGAAATGTCAACTTTGACGAGAACTGAAGAAGGAGAAAC
AAAAATCAAGATTCTTTCAAATCCAGAAGTTGATAAATTGATTGCAAATTATGAAAAGAT
TCAAGCTGAAGAGGAAGCAGCAAAGAAAGAAAAACTGGCTCAACAACAAGCACAGCAGCA
ACAAAAATCTTAATCATTTTGTATGGGCTGAAAGTTTCCATTTCTCTTTTTTAAAAAGAA
ATAAAATTTATTAATCATTTATTCACTTAAAA

>g4076.t9 Gene=g4076 Length=156
MARRYDSRTTIFSPEGRLYQVEYAMEAISHAGTCLGILAKDGILLAAERRNINKLLDNSI
FAEKIYRLNEDMVCSVAGITSDANVLTNELRLIAQRYQLQYDEPIPVEQLVSSLCDLKQA
YTQYGGKRPFGVSILYMGWDKHYGYQLYQSDPTRIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4076.t9 Gene3D G3DSA:3.60.20.10 Glutamine Phosphoribosylpyrophosphate 1 153 7.9E-66
3 g4076.t9 PANTHER PTHR11599:SF13 PROTEASOME SUBUNIT ALPHA TYPE-4 1 153 1.6E-73
4 g4076.t9 PANTHER PTHR11599 PROTEASOME SUBUNIT ALPHA/BETA 1 153 1.6E-73
2 g4076.t9 Pfam PF10584 Proteasome subunit A N-terminal signature 5 27 8.8E-14
1 g4076.t9 Pfam PF00227 Proteasome subunit 29 152 3.1E-40
7 g4076.t9 ProSitePatterns PS00388 Proteasome alpha-type subunits signature. 5 27 -
8 g4076.t9 ProSitePatterns PS00854 Proteasome beta-type subunits signature. 35 82 -
10 g4076.t9 ProSiteProfiles PS51475 Proteasome alpha-type subunit profile. 20 156 55.26
6 g4076.t9 SMART SM00948 Proteasome_A_N_2 5 27 3.4E-11
5 g4076.t9 SUPERFAMILY SSF56235 N-terminal nucleophile aminohydrolases (Ntn hydrolases) 4 152 3.66E-57

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:0019773 proteasome core complex, alpha-subunit complex CC
GO:0051603 proteolysis involved in cellular protein catabolic process BP
GO:0006511 ubiquitin-dependent protein catabolic process BP
GO:0004298 threonine-type endopeptidase activity MF
GO:0005839 proteasome core complex 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