Gene loci information

Transcript annotation

  • This transcript has been annotated as 26S proteasome regulatory subunit 6B.

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_1 g11790 g11790.t8 TTS g11790.t8 18445527 18445527
chr_1 g11790 g11790.t8 isoform g11790.t8 18445624 18447039
chr_1 g11790 g11790.t8 exon g11790.t8.exon1 18445624 18446807
chr_1 g11790 g11790.t8 cds g11790.t8.CDS1 18445624 18446424
chr_1 g11790 g11790.t8 exon g11790.t8.exon2 18447007 18447039
chr_1 g11790 g11790.t8 TSS g11790.t8 18447113 18447113

Sequences

>g11790.t8 Gene=g11790 Length=1217
ATGGCAGAAATTGAAGCAATTGCAGTAGATAAGGTGAGTAAATTATAACACCAAATTGGA
AAAACTAATTTTATATCTTACATTATATTTTAAAGAAATTACAAAAACAATTGGAATTTT
TGGAAGTTCAAGAAGAGTACATTAAAGATGAACAGCGTAATTTAAAGAAAGAGTATTTAC
ATGCACAAGAAGAAGTAAAGAGAATTCAATCAGTTCCACTTGTGATTGGTCAATTTTTAG
AAGCGGTTGATCAAAATACTGGTATAGTAGGATCTACTACTGGATCAAATTATTATGTTC
GAATTCTATCAACAATCGATCGTGAACTTTTAAAACCTTCAGCAAGTGTGGCACTACATA
AACATAGTAATGCACTTGTCGATGTTCTACCACCCGAGGCAGACAGCTCAATTTCCATGC
TTCAACCTGATGAAAAACCAGATGTTCAATATAGTGATATCGGTGGCATGGATATGCAAA
AACAAGAAATTCGTGAAGCAGTTGAACTTCCTTTAACTCACTTCGAGTTATACAAACAAA
TTGGTATTGATCCACCTCGAGGTGTGCTAATGTTTGGACCGCCTGGTTGTGGCAAAACAA
TGTTGGCTAAAGCTGTTGCTCATCATACTACTGCTGCGTTTATTCGAGTTGTTGGATCAG
AATTTGTACAAAAATATCTTGGTGAAGGTCCAAGGATGGTTCGAGATGTGTTTCGTTTAG
CAAAAGAAAATTCACCAGCAATCATTTTCATTGATGAGATTGATGCGATTGCTACTAAAC
GTTTTGATGCACAAACTGGTGCCGATCGAGAGGTTCAACGAATTCTGCTTGAGTTACTTA
ATCAAATGGACGGTTTTGATCAAACCACAAATGTGAAAGTAATTATGGCAACAAATCGAG
CTGATACATTAGATCCAGCACTGCTTCGTCCTGGTCGTTTGGATCGTAAAATTGAATTTC
CTTTGCCGGATAGACGTCAAAAACGTTTGATTTTTTCAACAATTACTTCAAAAATGAATT
TATCAGAAGATGTTGATTTGGAAGATTATGTTGCTCGACCTGATAAAATATCGGGAGCTG
ATATTAATGCAATTTGCCAAGAAGCAGGTATGCATGCTGTACGTGAAAATCGATATATTG
TTTTAGCAAAAGACTTTGAAAAAGGCTACAAGAATAATATCAAGAAAGATGAGCAAGAAC
ACGAGTTTTACAAATAA

>g11790.t8 Gene=g11790 Length=266
MLQPDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFELYKQIGIDPPRGVLMFGPPGCGK
TMLAKAVAHHTTAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENSPAIIFIDEIDAIAT
KRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIE
FPLPDRRQKRLIFSTITSKMNLSEDVDLEDYVARPDKISGADINAICQEAGMHAVRENRY
IVLAKDFEKGYKNNIKKDEQEHEFYK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11790.t8 CDD cd00009 AAA 16 183 6.02265E-28
9 g11790.t8 Gene3D G3DSA:3.40.50.300 - 1 183 9.9E-69
10 g11790.t8 Gene3D G3DSA:1.10.8.60 - 187 266 7.4E-24
3 g11790.t8 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 3 266 4.4E-165
4 g11790.t8 PANTHER PTHR23073:SF95 - 3 266 4.4E-165
7 g11790.t8 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 50 68 2.4E-5
5 g11790.t8 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 122 140 2.4E-5
6 g11790.t8 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 149 163 2.4E-5
1 g11790.t8 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 50 183 8.1E-44
2 g11790.t8 Pfam PF17862 AAA+ lid domain 205 249 3.9E-12
12 g11790.t8 ProSitePatterns PS00674 AAA-protein family signature. 153 171 -
13 g11790.t8 SMART SM00382 AAA_5 46 185 1.4E-23
8 g11790.t8 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 8 257 6.69E-67
14 g11790.t8 TIGRFAM TIGR01242 26Sp45: 26S proteasome subunit P45 family 5 250 3.9E-113

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:0030163 protein catabolic process BP
GO:0005737 cytoplasm CC
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