Gene loci information

Transcript annotation

  • This transcript has been annotated as 26S proteasome regulatory subunit 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 g1602 g1602.t11 TTS g1602.t11 12086105 12086105
chr_3 g1602 g1602.t11 isoform g1602.t11 12086169 12087914
chr_3 g1602 g1602.t11 exon g1602.t11.exon1 12086169 12086711
chr_3 g1602 g1602.t11 cds g1602.t11.CDS1 12086169 12086711
chr_3 g1602 g1602.t11 exon g1602.t11.exon2 12086767 12086869
chr_3 g1602 g1602.t11 cds g1602.t11.CDS2 12086767 12086869
chr_3 g1602 g1602.t11 exon g1602.t11.exon3 12086934 12087171
chr_3 g1602 g1602.t11 cds g1602.t11.CDS3 12086934 12087171
chr_3 g1602 g1602.t11 exon g1602.t11.exon4 12087358 12087509
chr_3 g1602 g1602.t11 cds g1602.t11.CDS4 12087358 12087478
chr_3 g1602 g1602.t11 exon g1602.t11.exon5 12087559 12087784
chr_3 g1602 g1602.t11 exon g1602.t11.exon6 12087912 12087914
chr_3 g1602 g1602.t11 TSS g1602.t11 12088004 12088004

Sequences

>g1602.t11 Gene=g1602 Length=1265
ATGGGCCAAAATCAATCTTCTGGTAGTGGAGATAAAAAAGATGATAAAGACAAGAAGAAG
AAGTACGAGCCACCAATTCCAACTCGCGTTGGTAAAAAGAAGCGAAAACAGAAGGGACCA
GATGCTGCATTAAAACTTCCGCAAGTCACTCCGCATACTCGTTGTCGTTTGAAATTGCTT
AAACTTGAACGCATCAAAGATTACCTTCTTATGGAAGAGGAATTTATTCGTCGAAAGTTG
ATGATTTGAGAGGAACACCAATGTCTGTTGGTAATCTGGAAGAAATCATTGATGATAATC
ATGCAATTGTTTCAACATCAGTTGGTAGTGAGCATTACGTTAGCATATTATCATTTGTCG
ATAAAGATCAACTTGAACCAGGATGTTCGGTCTTATTAAATCATAAAGTTCATGCTGTAG
TTGGTGTATTAAGTGATGATACAGATCCAATGGTTACGGTAATGAAATTAGAAAAAGCTC
CACAAGAAACTTATGCCGATATTGGCGGATTAGATACGCAAATTCAAGAAATTAAAGAGT
CTGTTGAATTACCTTTAACACATCCTGAATATTATGAAGAAATGGGTATTAAACCACCAA
AAGGAGTCATTTTATATGGTCCACCAGGTACAGGCAAAACTTTACTTGCTAAAGCTGTAG
CTAATCAGACATCAGCTACTTTCCTACGTGTTGTTGGATCAGAATTAATTCAAAAGTATT
TGGGTGATGGTCCAAAATTAGTTCGTGAATTGTTTCGCGTTGCAGAAGAACACGCACCAT
CTATCGTTTTTATTGATGAAATTGATGCAGTTGGCACAAAACGTTATGATTCAAATTCAG
GCGGTGAGAGAGAAATTCAAAGAACTATGTTGGAGTTGCTTAATCAATTAGATGGTTTTG
ATTCACGTGGTGATGTGAAAGTTATTATGGCAACAAATAGAATTGAAACTCTTGATCCTG
CTCTCATTCGTCCCGGACGTATTGATCGTAAAATTGAATTCCCTCTGCCAGATGAGAAGA
CAAAGAGAAGAATTTTCAATATTCACACTTCAAAAATGACACTCGCATCCGATGTCAATC
TTTCTGAATTAATTATGGCAAAAGATGATTTGTCTGGGGCTGATATAAAAGCTATTTGTA
CTGAAGCTGGTTTGATGGCTTTGCGTGAACGTCGAATGAAGGTTACAAATGATGACTTTA
AGAAATCGAAAGAGAGTGTACTTTATCGTAAAAAAGAAGGAACCCCAGATGGTTTATATT
TGTAA

>g1602.t11 Gene=g1602 Length=334
MSVGNLEEIIDDNHAIVSTSVGSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVVGVLSDD
TDPMVTVMKLEKAPQETYADIGGLDTQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYG
PPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDE
IDAVGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGR
IDRKIEFPLPDEKTKRRIFNIHTSKMTLASDVNLSELIMAKDDLSGADIKAICTEAGLMA
LRERRMKVTNDDFKKSKESVLYRKKEGTPDGLYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1602.t11 CDD cd00009 AAA 82 249 3.32928E-29
9 g1602.t11 Gene3D G3DSA:2.40.50.140 - 1 68 4.0E-29
7 g1602.t11 Gene3D G3DSA:3.40.50.300 - 69 249 4.8E-69
8 g1602.t11 Gene3D G3DSA:1.10.8.60 - 254 330 4.3E-22
4 g1602.t11 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 1 333 4.2E-213
5 g1602.t11 PANTHER PTHR23073:SF77 26S PROTEASOME REGULATORY SUBUNIT 4 1 333 4.2E-213
1 g1602.t11 Pfam PF16450 Proteasomal ATPase OB C-terminal domain 3 57 3.3E-11
2 g1602.t11 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 116 249 1.1E-42
3 g1602.t11 Pfam PF17862 AAA+ lid domain 271 315 4.5E-11
11 g1602.t11 ProSitePatterns PS00674 AAA-protein family signature. 219 237 -
12 g1602.t11 SMART SM00382 AAA_5 112 251 1.4E-22
6 g1602.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 74 326 1.22E-67
13 g1602.t11 TIGRFAM TIGR01242 26Sp45: 26S proteasome subunit P45 family 3 320 2.8E-137

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. There were no conditions that were differentially expressed