Gene loci information

Transcript annotation

  • This transcript has been annotated as AP-1 complex subunit sigma-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 g4969 g4969.t4 TTS g4969.t4 6203621 6203621
chr_2 g4969 g4969.t4 isoform g4969.t4 6203807 6209196
chr_2 g4969 g4969.t4 exon g4969.t4.exon1 6203807 6203851
chr_2 g4969 g4969.t4 cds g4969.t4.CDS1 6203807 6203851
chr_2 g4969 g4969.t4 exon g4969.t4.exon2 6208512 6208649
chr_2 g4969 g4969.t4 cds g4969.t4.CDS2 6208512 6208649
chr_2 g4969 g4969.t4 exon g4969.t4.exon3 6208708 6208816
chr_2 g4969 g4969.t4 cds g4969.t4.CDS3 6208708 6208816
chr_2 g4969 g4969.t4 exon g4969.t4.exon4 6208870 6209196
chr_2 g4969 g4969.t4 cds g4969.t4.CDS4 6208870 6209039
chr_2 g4969 g4969.t4 TSS g4969.t4 6209271 6209271

Sequences

>g4969.t4 Gene=g4969 Length=619
ATGGTAAGTAATGTTGAAAAAGTGAATATTAAATCATTATTATTATGTAGATTATTAAGT
TTTTCTTAAATAATAAGAATTCTTGCGAGAAATTACGTTTTTATAAAAATCAATAAATGT
CCGACATTAAAATTTCAATTTTTTGTAGATGCAATTTATGTTATTATTTAGCCGACAAGG
CAAATTAAGATTACAAAAGTGGTATGTAGCTCATCAAGATAAAGTAAAGAAGAAGATTAC
AAGAGAATTGATTTCTACAATACTTGCTCGCAAGCCGAAGATGTGCTCGTTTTTAGAGTA
CAAAGAATCTAAAATTGTGTATAAGAGATATGCAAGTTTATATTTCTGCTGTGCAGTTGA
GCAAGAAGACAATGAATTATTGACGCTTGAAATCATCCATCGGTACGTGGAACTTTTAGA
CAAATACTTTGGAAGCGTCTGTGAATTAGATATCATCTTCAATTTTGAAAAGGCATATTT
TATTCTCGATGAGCTATTGGTTGGCGGTGAGATACAAGAAACATCTAAGAAAAATGTTTT
GAAGGCAATTGCAGCACAAGATGTCTTGCAAGAGGATGAAACGCCTCAAGGATTTTTCGA
AGATCATGGACTTGGTTAA

>g4969.t4 Gene=g4969 Length=153
MLLFSRQGKLRLQKWYVAHQDKVKKKITRELISTILARKPKMCSFLEYKESKIVYKRYAS
LYFCCAVEQEDNELLTLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDELLVGGEIQ
ETSKKNVLKAIAAQDVLQEDETPQGFFEDHGLG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4969.t4 CDD cd14831 AP1_sigma 1 141 2.92004E-100
6 g4969.t4 Gene3D G3DSA:3.30.450.60 - 1 151 3.7E-59
2 g4969.t4 PANTHER PTHR11753 ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY 1 142 5.2E-85
3 g4969.t4 PANTHER PTHR11753:SF45 AP-1 COMPLEX SUBUNIT SIGMA-2 1 142 5.2E-85
7 g4969.t4 PIRSF PIRSF015588 AP_complex_sigma 1 146 6.7E-66
1 g4969.t4 Pfam PF01217 Clathrin adaptor complex small chain 1 136 1.2E-55
5 g4969.t4 ProSitePatterns PS00989 Clathrin adaptor complexes small chain signature. 53 63 -
4 g4969.t4 SUPERFAMILY SSF64356 SNARE-like 2 136 5.04E-43

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:0006886 intracellular protein transport BP
GO:0030117 membrane coat CC
GO:0015031 protein transport BP
GO:0016192 vesicle-mediated transport BP

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