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.t1 TTS g11790.t1 18445527 18445527
chr_1 g11790 g11790.t1 isoform g11790.t1 18445624 18447039
chr_1 g11790 g11790.t1 exon g11790.t1.exon1 18445624 18446745
chr_1 g11790 g11790.t1 cds g11790.t1.CDS1 18445624 18446745
chr_1 g11790 g11790.t1 exon g11790.t1.exon2 18446808 18446891
chr_1 g11790 g11790.t1 cds g11790.t1.CDS2 18446808 18446891
chr_1 g11790 g11790.t1 exon g11790.t1.exon3 18447007 18447039
chr_1 g11790 g11790.t1 cds g11790.t1.CDS3 18447007 18447039
chr_1 g11790 g11790.t1 TSS g11790.t1 18447113 18447113

Sequences

>g11790.t1 Gene=g11790 Length=1239
ATGGCAGAAATTGAAGCAATTGCAGTAGATAAGGAGGAAGCCACTGATGCAAATAAATCT
GTAAAAGAACCAAGCTTAGAAGAGCTTGATGTAGAAGATTTGTATACAAAATATAAGAAA
TTACAAAAACAATTGGAATTTTTGGAAGTTCAAGAAGAGTACATTAAAGATGAACAGCGT
AATTTAAAGAAAGAGTATTTACATGCACAAGAAGAAGTAAAGAGAATTCAATCAGTTCCA
CTTGTGATTGGTCAATTTTTAGAAGCGGTTGATCAAAATACTGGTATAGTAGGATCTACT
ACTGGATCAAATTATTATGTTCGAATTCTATCAACAATCGATCGTGAACTTTTAAAACCT
TCAGCAAGTGTGGCACTACATAAACATAGTAATGCACTTGTCGATGTTCTACCACCCGAG
GCAGACAGCTCAATTTCCATGCTTCAACCTGATGAAAAACCAGATGTTCAATATAGTGAT
ATCGGTGGCATGGATATGCAAAAACAAGAAATTCGTGAAGCAGTTGAACTTCCTTTAACT
CACTTCGAGTTATACAAACAAATTGGTATTGATCCACCTCGAGGTGTGCTAATGTTTGGA
CCGCCTGGTTGTGGCAAAACAATGTTGGCTAAAGCTGTTGCTCATCATACTACTGCTGCG
TTTATTCGAGTTGTTGGATCAGAATTTGTACAAAAATATCTTGGTGAAGGTCCAAGGATG
GTTCGAGATGTGTTTCGTTTAGCAAAAGAAAATTCACCAGCAATCATTTTCATTGATGAG
ATTGATGCGATTGCTACTAAACGTTTTGATGCACAAACTGGTGCCGATCGAGAGGTTCAA
CGAATTCTGCTTGAGTTACTTAATCAAATGGACGGTTTTGATCAAACCACAAATGTGAAA
GTAATTATGGCAACAAATCGAGCTGATACATTAGATCCAGCACTGCTTCGTCCTGGTCGT
TTGGATCGTAAAATTGAATTTCCTTTGCCGGATAGACGTCAAAAACGTTTGATTTTTTCA
ACAATTACTTCAAAAATGAATTTATCAGAAGATGTTGATTTGGAAGATTATGTTGCTCGA
CCTGATAAAATATCGGGAGCTGATATTAATGCAATTTGCCAAGAAGCAGGTATGCATGCT
GTACGTGAAAATCGATATATTGTTTTAGCAAAAGACTTTGAAAAAGGCTACAAGAATAAT
ATCAAGAAAGATGAGCAAGAACACGAGTTTTACAAATAA

>g11790.t1 Gene=g11790 Length=412
MAEIEAIAVDKEEATDANKSVKEPSLEELDVEDLYTKYKKLQKQLEFLEVQEEYIKDEQR
NLKKEYLHAQEEVKRIQSVPLVIGQFLEAVDQNTGIVGSTTGSNYYVRILSTIDRELLKP
SASVALHKHSNALVDVLPPEADSSISMLQPDEKPDVQYSDIGGMDMQKQEIREAVELPLT
HFELYKQIGIDPPRGVLMFGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYLGEGPRM
VRDVFRLAKENSPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVK
VIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEDVDLEDYVAR
PDKISGADINAICQEAGMHAVRENRYIVLAKDFEKGYKNNIKKDEQEHEFYK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11790.t1 CDD cd00009 AAA 162 329 3.81278E-27
13 g11790.t1 Coils Coil Coil 31 65 -
12 g11790.t1 Gene3D G3DSA:2.40.50.140 - 39 148 4.3E-30
10 g11790.t1 Gene3D G3DSA:3.40.50.300 - 149 329 2.4E-68
11 g11790.t1 Gene3D G3DSA:1.10.8.60 - 333 412 1.6E-23
4 g11790.t1 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 23 411 6.4E-235
5 g11790.t1 PANTHER PTHR23073:SF120 26S PROTEASOME REGULATORY SUBUNIT 6B HOMOLOG 23 411 6.4E-235
7 g11790.t1 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 196 214 7.0E-5
6 g11790.t1 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 268 286 7.0E-5
8 g11790.t1 PRINTS PR00300 ATP-dependent Clp protease ATP-binding subunit signature 295 309 7.0E-5
1 g11790.t1 Pfam PF16450 Proteasomal ATPase OB C-terminal domain 83 138 1.0E-10
2 g11790.t1 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 196 329 2.2E-43
3 g11790.t1 Pfam PF17862 AAA+ lid domain 351 395 7.5E-12
15 g11790.t1 ProSitePatterns PS00674 AAA-protein family signature. 299 317 -
16 g11790.t1 SMART SM00382 AAA_5 192 331 1.4E-23
9 g11790.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 154 401 3.18E-66
17 g11790.t1 TIGRFAM TIGR01242 26Sp45: 26S proteasome subunit P45 family 39 396 6.8E-138

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

Pathway

  • This transcript belongs to the following pathways

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