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.t7 isoform g4969.t7 6206011 6209196
chr_2 g4969 g4969.t7 exon g4969.t7.exon1 6206011 6206684
chr_2 g4969 g4969.t7 TTS g4969.t7 6206045 6206045
chr_2 g4969 g4969.t7 cds g4969.t7.CDS1 6206649 6206684
chr_2 g4969 g4969.t7 exon g4969.t7.exon2 6208512 6208649
chr_2 g4969 g4969.t7 cds g4969.t7.CDS2 6208512 6208649
chr_2 g4969 g4969.t7 exon g4969.t7.exon3 6208708 6208816
chr_2 g4969 g4969.t7 cds g4969.t7.CDS3 6208708 6208816
chr_2 g4969 g4969.t7 exon g4969.t7.exon4 6208870 6209048
chr_2 g4969 g4969.t7 cds g4969.t7.CDS4 6208870 6209048
chr_2 g4969 g4969.t7 exon g4969.t7.exon5 6209194 6209196
chr_2 g4969 g4969.t7 cds g4969.t7.CDS5 6209194 6209196
chr_2 g4969 g4969.t7 TSS g4969.t7 6209271 6209271

Sequences

>g4969.t7 Gene=g4969 Length=1103
ATGATGCAATTTATGTTATTATTTAGCCGACAAGGCAAATTAAGATTACAAAAGTGGTAT
GTAGCTCATCAAGATAAAGTAAAGAAGAAGATTACAAGAGAATTGATTTCTACAATACTT
GCTCGCAAGCCGAAGATGTGCTCGTTTTTAGAGTACAAAGAATCTAAAATTGTGTATAAG
AGATATGCAAGTTTATATTTCTGCTGTGCAGTTGAGCAAGAAGACAATGAATTATTGACG
CTTGAAATCATCCATCGGTACGTGGAACTTTTAGACAAATACTTTGGAAGCGTCTGTGAA
TTAGATATCATCTTCAATTTTGAAAAGGCATATTTTATTCTCGATGAGCTATTGGTTGGC
GGTGAGATACAAGAAACATCTAAGAAAAATGTTTTGAAGGCAATTGCAGCACAAGATGTC
TTGCAAGAGGTTCTAGATGAGGAAGATTATTTTTTCTTTTATTAGTCATGATTCTTACCA
AAAAAATATATAATTATTGTTTCTAGTTTTATTATATAAACATTATTTTTTCCTATTTGA
CGGCTATTATAATAATTAAAGAGAACAGATTTATCATACCTAGTCTTTTTTGATAATGAG
TAAATTTTTTTGTAAACTTGGGTATTGGCAATGAAATGAAAATATTCATAGAAAAATCAG
CAAAAATGTATCAACATCCTTTCATCCTAATAGTGTCAAAATAAAATGCTCAACAAAGTA
AGAATTCATCCACAAAGAAAAACCATTCATTTAAATTCCTTGCCAATATTCGACAAAAAA
ATATATAATATGAAAATTGTCCAGTATTTATTATTCACAAGCATTCTAAATGTAAAACAA
AAAAATCAACCTTGTAAATTAAGATTCTTTTTAAGCGCGCCACTATAAATTGCCCATGTT
TTTAAAAGACAATTAAGAAAATTCTTAAATATTGAACATTTATATTTTTTCACAATTTTT
ATTATCTCAAATCATTTTTAAACTGAAAAAGAAAACTATTGTTATAATGCCAAATGAAAC
TAAACAGTAAAACAAAATTAAAATGAATCATTAATGTAATGAAAATAATAAAAATTAAAA
TGCCTTTTTATTTTTATCGTTTA

>g4969.t7 Gene=g4969 Length=154
MMQFMLLFSRQGKLRLQKWYVAHQDKVKKKITRELISTILARKPKMCSFLEYKESKIVYK
RYASLYFCCAVEQEDNELLTLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDELLVG
GEIQETSKKNVLKAIAAQDVLQEVLDEEDYFFFY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4969.t7 CDD cd14831 AP1_sigma 3 143 2.92128E-98
6 g4969.t7 Gene3D G3DSA:3.30.450.60 - 1 151 7.3E-60
2 g4969.t7 PANTHER PTHR11753 ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY 2 147 5.9E-87
3 g4969.t7 PANTHER PTHR11753:SF45 AP-1 COMPLEX SUBUNIT SIGMA-2 2 147 5.9E-87
7 g4969.t7 PIRSF PIRSF015588 AP_complex_sigma 1 151 7.4E-67
1 g4969.t7 Pfam PF01217 Clathrin adaptor complex small chain 1 140 1.9E-57
5 g4969.t7 ProSitePatterns PS00989 Clathrin adaptor complexes small chain signature. 57 67 -
4 g4969.t7 SUPERFAMILY SSF64356 SNARE-like 1 140 6.41E-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