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.t8 TTS g1602.t8 12086105 12086105
chr_3 g1602 g1602.t8 isoform g1602.t8 12086169 12087914
chr_3 g1602 g1602.t8 exon g1602.t8.exon1 12086169 12086711
chr_3 g1602 g1602.t8 cds g1602.t8.CDS1 12086169 12086711
chr_3 g1602 g1602.t8 exon g1602.t8.exon2 12086767 12086869
chr_3 g1602 g1602.t8 cds g1602.t8.CDS2 12086767 12086869
chr_3 g1602 g1602.t8 exon g1602.t8.exon3 12086934 12087171
chr_3 g1602 g1602.t8 cds g1602.t8.CDS3 12086934 12087171
chr_3 g1602 g1602.t8 exon g1602.t8.exon4 12087358 12087914
chr_3 g1602 g1602.t8 cds g1602.t8.CDS4 12087358 12087577
chr_3 g1602 g1602.t8 TSS g1602.t8 12088004 12088004

Sequences

>g1602.t8 Gene=g1602 Length=1441
ATGGTAAGTCATTTATTAAATATCTAAGTAATGGTAATAAACTTAAATTTCAATAAAATT
TGATCAATTTCACATGAAATTCATGTAAAAAATTTTCATTAAAATAAATTCTTTTAATTG
AAAATAATAGGGCCAAAATCAATCTTCTGGTAGTGGAGATAAAAAAGATGATAAAGACAA
GAAGAAGAAGTACGAGCCACCAATTCCAACTCGCGTTGGTAAAAAGAAGCGAAAACAGAA
GGGACCAGATGCTGCATTAAAACTTCCGCAAGTCACTCCGCATACTCGTTGTCGTTTGAA
ATTGCTTAAACTTGAACGCATCAAAGATTACCTTCTTATGGAAGAGGAATTTATTCGTAA
TCAAGAGCGTTTGAAGCCTCAAGAAGAGAAGAATGAAGAAGAAAGGTCGAAAGTTGATGA
TTTGAGAGGAACACCAATGTCTGTTGGTAATCTGGAAGAAATCATTGATGATAATCATGC
AATTGTTTCAACATCAGTTGGTAGTGAGCATTACGTTAGCATATTATCATTTGTCGATAA
AGATCAACTTGAACCAGGATGTTCGGTCTTATTAAATCATAAAGTTCATGCTGTAGTTGG
TGTATTAAGTGATGATACAGATCCAATGGTTACGGTAATGAAATTAGAAAAAGCTCCACA
AGAAACTTATGCCGATATTGGCGGATTAGATACGCAAATTCAAGAAATTAAAGAGTCTGT
TGAATTACCTTTAACACATCCTGAATATTATGAAGAAATGGGTATTAAACCACCAAAAGG
AGTCATTTTATATGGTCCACCAGGTACAGGCAAAACTTTACTTGCTAAAGCTGTAGCTAA
TCAGACATCAGCTACTTTCCTACGTGTTGTTGGATCAGAATTAATTCAAAAGTATTTGGG
TGATGGTCCAAAATTAGTTCGTGAATTGTTTCGCGTTGCAGAAGAACACGCACCATCTAT
CGTTTTTATTGATGAAATTGATGCAGTTGGCACAAAACGTTATGATTCAAATTCAGGCGG
TGAGAGAGAAATTCAAAGAACTATGTTGGAGTTGCTTAATCAATTAGATGGTTTTGATTC
ACGTGGTGATGTGAAAGTTATTATGGCAACAAATAGAATTGAAACTCTTGATCCTGCTCT
CATTCGTCCCGGACGTATTGATCGTAAAATTGAATTCCCTCTGCCAGATGAGAAGACAAA
GAGAAGAATTTTCAATATTCACACTTCAAAAATGACACTCGCATCCGATGTCAATCTTTC
TGAATTAATTATGGCAAAAGATGATTTGTCTGGGGCTGATATAAAAGCTATTTGTACTGA
AGCTGGTTTGATGGCTTTGCGTGAACGTCGAATGAAGGTTACAAATGATGACTTTAAGAA
ATCGAAAGAGAGTGTACTTTATCGTAAAAAAGAAGGAACCCCAGATGGTTTATATTTGTA
A

>g1602.t8 Gene=g1602 Length=367
MEEEFIRNQERLKPQEEKNEEERSKVDDLRGTPMSVGNLEEIIDDNHAIVSTSVGSEHYV
SILSFVDKDQLEPGCSVLLNHKVHAVVGVLSDDTDPMVTVMKLEKAPQETYADIGGLDTQ
IQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGS
ELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAVGTKRYDSNSGGEREIQRTMLELL
NQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKRRIFNIHTSKMT
LASDVNLSELIMAKDDLSGADIKAICTEAGLMALRERRMKVTNDDFKKSKESVLYRKKEG
TPDGLYL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1602.t8 CDD cd00009 AAA 115 282 7.1245E-29
9 g1602.t8 Gene3D G3DSA:2.40.50.140 - 34 101 4.6E-29
7 g1602.t8 Gene3D G3DSA:3.40.50.300 - 102 282 6.1E-69
8 g1602.t8 Gene3D G3DSA:1.10.8.60 - 287 363 5.1E-22
13 g1602.t8 MobiDBLite mobidb-lite consensus disorder prediction 1 32 -
14 g1602.t8 MobiDBLite mobidb-lite consensus disorder prediction 1 29 -
4 g1602.t8 PANTHER PTHR23073 26S PROTEASOME REGULATORY SUBUNIT 1 366 4.2E-235
5 g1602.t8 PANTHER PTHR23073:SF77 26S PROTEASOME REGULATORY SUBUNIT 4 1 366 4.2E-235
1 g1602.t8 Pfam PF16450 Proteasomal ATPase OB C-terminal domain 36 90 3.8E-11
2 g1602.t8 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 149 282 1.3E-42
3 g1602.t8 Pfam PF17862 AAA+ lid domain 304 348 5.2E-11
11 g1602.t8 ProSitePatterns PS00674 AAA-protein family signature. 252 270 -
12 g1602.t8 SMART SM00382 AAA_5 145 284 1.4E-22
6 g1602.t8 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 107 359 1.63E-67
15 g1602.t8 TIGRFAM TIGR01242 26Sp45: 26S proteasome subunit P45 family 9 353 4.0E-141

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