Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable 26S proteasome non-ATPase regulatory subunit 3.

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 g4920 g4920.t6 TTS g4920.t6 5963285 5963285
chr_2 g4920 g4920.t6 isoform g4920.t6 5963398 5964937
chr_2 g4920 g4920.t6 exon g4920.t6.exon1 5963398 5964437
chr_2 g4920 g4920.t6 cds g4920.t6.CDS1 5963398 5964063
chr_2 g4920 g4920.t6 exon g4920.t6.exon2 5964501 5964937
chr_2 g4920 g4920.t6 TSS g4920.t6 5965056 5965056

Sequences

>g4920.t6 Gene=g4920 Length=1477
CAAAATGGTTGCAGTACAAGATGTGGAAATGGAAGTCATTGAAAGTGAAAATACAGAACA
GGAGCAACAGAAGAAAGAATCGGATGTGAATACAATTGTCCAAGAGATTCGAGAACATGT
AAAGCAAATTGATAAAGCAGTAGCAAGCAAAGAACCGCGTTTTATTCTTCGTGTTTTAAG
ATCTCTACCAAATACACGTAGAAAATTGACTCCCGTTGTTCTTAGATCACTCGCAAATCA
AATCTATCCTGTATCTGAACGAGATGCTATTCTTGTATATGTCGAGGAAGTAACTAGTGG
AGAGCAGCAAAATGAAAGTGCAAGTGCACGTCCTCGCGCAACAATTAAAACTCCACTTCC
AGAAGTTGATGCATATTTTCACTTATTAGCTCTTGTTCGTTTGTTAGACGCGAAATTGCT
TGATAAAGCATCTCATTCTCAACAGCTCATGACAAAAATTATGTCTCAGAATCGTAGATC
ATTAGATCTTATTGCTGCAAAGAGCTATTTCTATCATTCACGAGTTGCAGAATTAACAAA
TAAATTGGATACAATTCGTGGATTTTTACATGCTCGTCTAAGAACTGCAACTCTACGTAA
TGATTTTGAGGGATAAGCTGTCCTAATTAATTGTCTTTTACGCAATTACTTGCATTATTC
ATTATATGATCAAGCTGATAAATTAGTTAACAAATCAGTCTTTCCTGAAACTGCAAGTAA
CAATGAATGGGCCCGTTTTCTTTATTATTTGGGTCGTATAAAGGCTGCAAAATTGGAATA
TAGTGTTGCACATAAGCATCTTATTCAGGCTATGCGAAAGGCTCCACAAAATGCTGCAAT
TGGTTTCCGTCAAACAGTTCAGAAACTTGTAGTTGTTGTTGAATTACTTTTGGGTGATAT
CCCAGAACGACAAATTTTCAGACAAGCAGCTCTTCGTCGTTCACTCGTTCCTTATTTTCA
ACTTACACAAGCTGTAAGATTGGGAAATCTGAAACGTTTCGGTGAAGTGCTTACCAATTA
TGGTGAAAAATTCCGTCAAGATCATACATTTACACTCATCATTCGTTTGAGACATAATGT
CATTAAGACTGCAATAAGATCAATTGGACTCTCATATTCATGCATTTCACCAGCTGATAT
AGCCAAAAAATTAGGAATTGATTCTAAGGAGGATGCAGAATTTATTGTATCGAAAGCTAT
TCGTGATGGTGTTATTGAAGCAACATTAGATCCAGAAAAAGGATATATGCGCAGCAAAGA
GAGCACAGATATATATTCAACTCGTGAGCCTCAATTGGCTTTTCATCAACGCATCACTTT
CTGCTTAGATTTGCATAATCAATCAGTTAAAGCAATGCGATATCCACCAAAATCATATGG
CAAGGATTTGGAAAGTGCTGAAGAACGAATTGAACGTGAGCAACAAGAAGTTGAATTAGC
AAAGGAAATGGCAGAAGATGATGATGATGGTTTTTAA

>g4920.t6 Gene=g4920 Length=221
MRKAPQNAAIGFRQTVQKLVVVVELLLGDIPERQIFRQAALRRSLVPYFQLTQAVRLGNL
KRFGEVLTNYGEKFRQDHTFTLIIRLRHNVIKTAIRSIGLSYSCISPADIAKKLGIDSKE
DAEFIVSKAIRDGVIEATLDPEKGYMRSKESTDIYSTREPQLAFHQRITFCLDLHNQSVK
AMRYPPKSYGKDLESAEERIEREQQEVELAKEMAEDDDDGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4920.t6 Coils Coil Coil 193 217 -
6 g4920.t6 Gene3D G3DSA:1.25.40.570 - 1 96 7.7E-23
11 g4920.t6 MobiDBLite mobidb-lite consensus disorder prediction 185 204 -
10 g4920.t6 MobiDBLite mobidb-lite consensus disorder prediction 190 204 -
3 g4920.t6 PANTHER PTHR10758:SF2 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3 1 221 2.1E-109
4 g4920.t6 PANTHER PTHR10758 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 3/COP9 SIGNALOSOME COMPLEX SUBUNIT 3 1 221 2.1E-109
2 g4920.t6 Pfam PF01399 PCI domain 47 149 3.7E-21
1 g4920.t6 Pfam PF08375 Proteasome regulatory subunit C-terminal 153 219 2.0E-28
12 g4920.t6 ProSiteProfiles PS50250 PCI domain profile. 1 153 22.531
8 g4920.t6 SMART SM00088 PINT_4 81 171 6.6E-26
9 g4920.t6 SMART SM00753 motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 81 171 6.6E-26
5 g4920.t6 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 86 153 7.89E-8

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:0000502 proteasome complex CC
GO:0042176 regulation of protein catabolic process BP
GO:0030234 enzyme regulator 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. There were no conditions that were differentially expressed