Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Peroxisome biogenesis factor 2.

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_2 g8121 g8121.t1 TTS g8121.t1 28673653 28673653
chr_2 g8121 g8121.t1 isoform g8121.t1 28673729 28674641
chr_2 g8121 g8121.t1 exon g8121.t1.exon1 28673729 28674034
chr_2 g8121 g8121.t1 cds g8121.t1.CDS1 28673729 28674034
chr_2 g8121 g8121.t1 exon g8121.t1.exon2 28674096 28674641
chr_2 g8121 g8121.t1 cds g8121.t1.CDS2 28674096 28674641
chr_2 g8121 g8121.t1 TSS g8121.t1 28674654 28674654

Sequences

>g8121.t1 Gene=g8121 Length=852
ATGGAAAACAAAACAGCATATGTTTCAAGAGTTAATCAATTAGATGCATATTTATTAGAC
AAAGAAATAGTTAAAATTATACAGGAACAGCTGTCTCATGCTTACAAAGAATTGCCACCT
GGAATTTTAAGCAAATTTCAACCAGAAATCGATGCATTGCTCAAAACGCTCATTTGGCTT
AATTCTATTTTATTCAATAAATCCACATTTGGTCAACAAATTTTAGCTATTACATATCAA
AGCGATAAACTCACGAGAAACAAATTAATTCTTCATTATTTACTCACGATTCTTGCACCA
TACACTAGAGAATTTGGACATTTGAGGCTTACGAGTAACGTACATTTACAGAAAATAATT
TCTTGGATAGAATTTTGTGCTAAATTGTTAACTATCATCAACTTTTTCCGTTTTCTTAAA
ACTGGTCAATATCCGTCGCTAGTTGATTATTTTGTAAGATGGAAGCATATTTCACAGAGT
GGTGCACAAATGAGAAATTTTGGATATGCATATATGAACCGAGAGTTGATTTGGACTGGT
TTTCTGGAATTATTGAATGTGACTCTTCCTTTAGTAAATTATAATGTGATTCAAAGAAAA
ATAACACAGTTTTTAACATCGTCACAAAAAAATTGTCAAATTGTTTCTAAAATCAGTCCA
ATAATGACTATTGATACAAAATGTGCAATTTGTTCAAAAAGACCTTCAATTCCTCATCAC
ATAAATTGTCAGCATGTATTTTGTTACTTTTGCATTCAAGGAAATTTAATGATGGACTCA
GAATTTTCTTGTCCTATCTGTGATACAAAAAATAATGGCAATATTTATCCATTAGAAATG
AAAATGGAATAA

>g8121.t1 Gene=g8121 Length=283
MENKTAYVSRVNQLDAYLLDKEIVKIIQEQLSHAYKELPPGILSKFQPEIDALLKTLIWL
NSILFNKSTFGQQILAITYQSDKLTRNKLILHYLLTILAPYTREFGHLRLTSNVHLQKII
SWIEFCAKLLTIINFFRFLKTGQYPSLVDYFVRWKHISQSGAQMRNFGYAYMNRELIWTG
FLELLNVTLPLVNYNVIQRKITQFLTSSQKNCQIVSKISPIMTIDTKCAICSKRPSIPHH
INCQHVFCYFCIQGNLMMDSEFSCPICDTKNNGNIYPLEMKME

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g8121.t1 CDD cd16526 RING-HC_PEX2 227 267 1.17193E-15
6 g8121.t1 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 186 280 8.5E-10
3 g8121.t1 PANTHER PTHR23350 PEROXISOME ASSEMBLY PROTEIN 10 4 269 2.9E-52
4 g8121.t1 PANTHER PTHR23350:SF4 PEROXISOME BIOGENESIS FACTOR 2 4 269 2.9E-52
2 g8121.t1 Pfam PF04757 Pex2 / Pex12 amino terminal region 20 207 2.1E-20
1 g8121.t1 Pfam PF00097 Zinc finger, C3HC4 type (RING finger) 228 267 2.9E-6
8 g8121.t1 ProSitePatterns PS00518 Zinc finger RING-type signature. 243 252 -
10 g8121.t1 ProSiteProfiles PS50089 Zinc finger RING-type profile. 228 268 11.102
9 g8121.t1 SMART SM00184 ring_2 228 267 5.1E-5
5 g8121.t1 SUPERFAMILY SSF57850 RING/U-box 227 270 5.05E-10

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:0046872 metal ion binding 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