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.t12 TTS g4969.t12 6203621 6203621
chr_2 g4969 g4969.t12 isoform g4969.t12 6208054 6209196
chr_2 g4969 g4969.t12 exon g4969.t12.exon1 6208054 6208649
chr_2 g4969 g4969.t12 cds g4969.t12.CDS1 6208482 6208649
chr_2 g4969 g4969.t12 exon g4969.t12.exon2 6208708 6208816
chr_2 g4969 g4969.t12 cds g4969.t12.CDS2 6208708 6208816
chr_2 g4969 g4969.t12 exon g4969.t12.exon3 6208870 6209048
chr_2 g4969 g4969.t12 cds g4969.t12.CDS3 6208870 6209048
chr_2 g4969 g4969.t12 exon g4969.t12.exon4 6209194 6209196
chr_2 g4969 g4969.t12 cds g4969.t12.CDS4 6209194 6209196
chr_2 g4969 g4969.t12 TSS g4969.t12 6209271 6209271

Sequences

>g4969.t12 Gene=g4969 Length=887
ATGATGCAATTTATGTTATTATTTAGCCGACAAGGCAAATTAAGATTACAAAAGTGGTAT
GTAGCTCATCAAGATAAAGTAAAGAAGAAGATTACAAGAGAATTGATTTCTACAATACTT
GCTCGCAAGCCGAAGATGTGCTCGTTTTTAGAGTACAAAGAATCTAAAATTGTGTATAAG
AGATATGCAAGTTTATATTTCTGCTGTGCAGTTGAGCAAGAAGACAATGAATTATTGACG
CTTGAAATCATCCATCGGTACGTGGAACTTTTAGACAAATACTTTGGAAGCGTCTGTGAA
TTAGATATCATCTTCAATTTTGAAAAGGCATATTTTATTCTCGATGAGCTATTGGTTGGC
GGTGAGATACAAGAAACATCTAAGAAAAATGTTTTGAAGGCAATTGCAGCACAAGATGTC
TTGCAAGAGGTAGGGAATGATGAAACTTACGATATTTAAACTCTTAATTCAGTAATATAT
AAAACATTAATCATTTGAGTCGTTGTGTTATGAAAGAAAAGTCAATCAAAAAGTATATGA
AAGATGCTAATATCTCAATCTTGCCTTCGTCATTTAAAAATGTCTGACTTTCATTATACA
CAAATATAAAAGAAATGACGATAACAAACTTGCCAAATTATCTTATGCTTTATTTTTTTT
CTCGTAAAAGTTGATTTTTAAGTTGTTTTATATCTCAATTATGATTTTGCTCAGTATATC
AAATTTTTTGCTTTTTATAATGCATTCTTATAAAATTTTAAGGCAGGGATTAAGGTTGCA
ACTATAAAAAATAAATATTTTTCATAACTTTTATTGTTGTCTCTTTTAAAAGAGATATTA
AAGTATTTTTGCCTTTAAGCAAGACTATGATAAAAATTTCACCAAAA

>g4969.t12 Gene=g4969 Length=152
MMQFMLLFSRQGKLRLQKWYVAHQDKVKKKITRELISTILARKPKMCSFLEYKESKIVYK
RYASLYFCCAVEQEDNELLTLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDELLVG
GEIQETSKKNVLKAIAAQDVLQEVGNDETYDI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4969.t12 CDD cd14831 AP1_sigma 3 143 6.97021E-100
6 g4969.t12 Gene3D G3DSA:3.30.450.60 - 1 151 3.5E-60
2 g4969.t12 PANTHER PTHR11753 ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY 2 144 3.1E-87
3 g4969.t12 PANTHER PTHR11753:SF45 AP-1 COMPLEX SUBUNIT SIGMA-2 2 144 3.1E-87
7 g4969.t12 PIRSF PIRSF015588 AP_complex_sigma 1 151 2.6E-67
1 g4969.t12 Pfam PF01217 Clathrin adaptor complex small chain 1 140 1.8E-57
5 g4969.t12 ProSitePatterns PS00989 Clathrin adaptor complexes small chain signature. 57 67 -
4 g4969.t12 SUPERFAMILY SSF64356 SNARE-like 1 140 5.95E-45

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.

Raw TPM values