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.t2 TTS g11790.t2 18445527 18445527
chr_1 g11790 g11790.t2 isoform g11790.t2 18445624 18446402
chr_1 g11790 g11790.t2 exon g11790.t2.exon1 18445624 18446402
chr_1 g11790 g11790.t2 cds g11790.t2.CDS1 18445624 18446373
chr_1 g11790 g11790.t2 TSS g11790.t2 18447113 18447113

Sequences

>g11790.t2 Gene=g11790 Length=779
CAGATGTTCAATATAGTGATATCGGTGGCATGGATATGCAAAAACAAGAAATTCGTGAAG
CAGTTGAACTTCCTTTAACTCACTTCGAGTTATACAAACAAATTGGTATTGATCCACCTC
GAGGTGTGCTAATGTTTGGACCGCCTGGTTGTGGCAAAACAATGTTGGCTAAAGCTGTTG
CTCATCATACTACTGCTGCGTTTATTCGAGTTGTTGGATCAGAATTTGTACAAAAATATC
TTGGTGAAGGTCCAAGGATGGTTCGAGATGTGTTTCGTTTAGCAAAAGAAAATTCACCAG
CAATCATTTTCATTGATGAGATTGATGCGATTGCTACTAAACGTTTTGATGCACAAACTG
GTGCCGATCGAGAGGTTCAACGAATTCTGCTTGAGTTACTTAATCAAATGGACGGTTTTG
ATCAAACCACAAATGTGAAAGTAATTATGGCAACAAATCGAGCTGATACATTAGATCCAG
CACTGCTTCGTCCTGGTCGTTTGGATCGTAAAATTGAATTTCCTTTGCCGGATAGACGTC
AAAAACGTTTGATTTTTTCAACAATTACTTCAAAAATGAATTTATCAGAAGATGTTGATT
TGGAAGATTATGTTGCTCGACCTGATAAAATATCGGGAGCTGATATTAATGCAATTTGCC
AAGAAGCAGGTATGCATGCTGTACGTGAAAATCGATATATTGTTTTAGCAAAAGACTTTG
AAAAAGGCTACAAGAATAATATCAAGAAAGATGAGCAAGAACACGAGTTTTACAAATAA

>g11790.t2 Gene=g11790 Length=249
MDMQKQEIREAVELPLTHFELYKQIGIDPPRGVLMFGPPGCGKTMLAKAVAHHTTAAFIR
VVGSEFVQKYLGEGPRMVRDVFRLAKENSPAIIFIDEIDAIATKRFDAQTGADREVQRIL
LELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTIT
SKMNLSEDVDLEDYVARPDKISGADINAICQEAGMHAVRENRYIVLAKDFEKGYKNNIKK
DEQEHEFYK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11790.t2 CDD cd00009 AAA 1 166 8.28804E-27
9 g11790.t2 Gene3D G3DSA:3.40.50.300 - 1 166 1.4E-63
10 g11790.t2 Gene3D G3DSA:1.10.8.60 - 170 249 6.5E-24
3 g11790.t2 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 2 249 3.7E-157
4 g11790.t2 PANTHER PTHR23073:SF95 - 2 249 3.7E-157
6 g11790.t2 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 33 51 2.1E-5
7 g11790.t2 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 105 123 2.1E-5
5 g11790.t2 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 132 146 2.1E-5
1 g11790.t2 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 33 166 6.8E-44
2 g11790.t2 Pfam PF17862 AAA+ lid domain 188 232 3.6E-12
12 g11790.t2 ProSitePatterns PS00674 AAA-protein family signature. 136 154 -
13 g11790.t2 SMART SM00382 AAA_5 29 168 1.4E-23
8 g11790.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 4 240 6.27E-64
14 g11790.t2 TIGRFAM TIGR01242 26Sp45: 26S proteasome subunit P45 family 2 233 3.6E-105

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