Gene loci information

Transcript annotation

  • This transcript has been annotated as Peroxisome biosynthesis protein PAS1.

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 g780 g780.t3 isoform g780.t3 5982825 5983733
chr_3 g780 g780.t3 exon g780.t3.exon1 5982825 5983733
chr_3 g780 g780.t3 cds g780.t3.CDS1 5982891 5983733
chr_3 g780 g780.t3 TSS g780.t3 NA NA
chr_3 g780 g780.t3 TTS g780.t3 NA NA

Sequences

>g780.t3 Gene=g780 Length=909
GGAATAAAAACTGAATCAATTGATAGTGACGATGCACAAATTGATATAAAAGAGGAAATT
CCTGGTATGGATAATGTTATCGAAACACTTGAAGAAGTCTTAATATGGCCAACAAAGTTT
TCAAAAATATTTCAAAATTCACCATTGAGAAATCAAGCGGGCATTCTGTTATTTGGTTTT
CCAGGTTCGGGAAAAAATTTTATTGTCTCACAAATAACAAAACGATGGAATTTAAGATTA
ATATCAATTAAAGGACCAGAACTATTGGCAAAATATATTGGTCAAAGTGAAGAGAATGTG
AGAAATTTGTTTGAGAAAGCAAAATCAGCCAAACCATGTGTTCTCTTCTTTGATGAATTT
GAGAGTTTAGCACCACGAAGGGGTCACGACTCGACTGGCGTTACTGACAGAGTCGTTAAT
CAACTGTTAACAGAATTGGATGGTGTAAAAAGTTTAGAAGGAGTTTCAATTATATGTGCT
ACCTCTAGACCCGATCTTATCGATCCTGCATTATTACGTAGTGGAAGAATTGATCGTTTG
GTTGAATGTCAATTGCCAAATGCATCCGAAAGATTGGATATTTTGAAATATTTATCTAAA
TCTTTATTAATAGACTCAAATGTGGACTTTAAAGTTCTAGCATCAAAAATGACTACATTC
ACTGGAGCTGATATTAAAAGTGTACTAACAACAGCAAATATGAATGCTATCGAAGAAGAA
ATAAAGAAAAATAATGGAAGAGCGATAGAAAATGTTGAAATTAAGCAAACTCATTTAGAA
GCAGCTTTTCAAAATACTCGTGCTTCTTTAACTAAACAGGATATTGAAAAATATCAAATG
CTTTATGATAGATTCAAAAACAAAAAGTCTGTAACAGTTGAAACACCACAACGTGTTAGT
TTAGCATAA

>g780.t3 Gene=g780 Length=280
MDNVIETLEEVLIWPTKFSKIFQNSPLRNQAGILLFGFPGSGKNFIVSQITKRWNLRLIS
IKGPELLAKYIGQSEENVRNLFEKAKSAKPCVLFFDEFESLAPRRGHDSTGVTDRVVNQL
LTELDGVKSLEGVSIICATSRPDLIDPALLRSGRIDRLVECQLPNASERLDILKYLSKSL
LIDSNVDFKVLASKMTTFTGADIKSVLTTANMNAIEEEIKKNNGRAIENVEIKQTHLEAA
FQNTRASLTKQDIEKYQMLYDRFKNKKSVTVETPQRVSLA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g780.t3 CDD cd00009 AAA 1 163 3.01092E-21
8 g780.t3 Gene3D G3DSA:3.40.50.300 - 1 163 9.5E-53
9 g780.t3 Gene3D G3DSA:1.10.8.60 - 164 265 1.3E-20
3 g780.t3 PANTHER PTHR23077 AAA-FAMILY ATPASE 2 263 7.6E-108
4 g780.t3 PANTHER PTHR23077:SF12 PEROXISOME BIOGENESIS FACTOR 1 2 263 7.6E-108
1 g780.t3 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 33 161 4.2E-38
2 g780.t3 Pfam PF17862 AAA+ lid domain 185 222 3.8E-7
7 g780.t3 ProSitePatterns PS00674 AAA-protein family signature. 133 151 -
6 g780.t3 SMART SM00382 AAA_5 29 165 5.7E-11
5 g780.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 263 1.29E-53

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:0006625 protein targeting to peroxisome BP
GO:0016887 ATP hydrolysis activity MF
GO:0005778 peroxisomal membrane CC

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