Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Translocation protein SEC62.

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 g6650 g6650.t19 TTS g6650.t19 17941016 17941016
chr_2 g6650 g6650.t19 isoform g6650.t19 17941626 17943095
chr_2 g6650 g6650.t19 exon g6650.t19.exon1 17941626 17942334
chr_2 g6650 g6650.t19 cds g6650.t19.CDS1 17941627 17942181
chr_2 g6650 g6650.t19 exon g6650.t19.exon2 17943065 17943095
chr_2 g6650 g6650.t19 TSS g6650.t19 17943212 17943212

Sequences

>g6650.t19 Gene=g6650 Length=740
ATGTCGGGAAAAGATAAAAGAGTCAATAAAAGAATATAAAGAGAATGATGACGAGCAGGA
AAAGGCAAGTAAAGAAGAGTATAAAGTTGCCAAGTGGATACGCAACAATGTTCCCGTGAA
AAAAACTAAATTTCTCAATCACAATGTTGAATATTTTACATCAGCAAAAGCGCTTGATGC
TCTGATGACATCAAAATTCGCCCAAGGTGATAATTGTCTTTTTCCAACACGTCAAATTGC
AATTGATTATATGGATAAAATGCTTGCACATAAATTTTTTCATCGTGCAAAAAAGATACC
TGTTAGTGAGATGGAATTGAGAGGTGGACGCACAAAAGACAAATCAAAAGATCAAGAGAA
AAAAGAAACAGATGCTGAAAGCTCACATGAGAAAGACAAAAGCGATAAAGCAACATCAGA
AAAGAAAAAAAGGAAAATTCGCTTGGAAATGCATCCACAACAGATTTTTATCGATGGACA
TGAAGCATATGTCTGGATTTATGATCCTATTCCGATGACTTATTGGATCTTTGGAGCTCT
TGTTGTAATTGGAGCAATAGTCATCTGTTTATTCCCACTCTGGCCACCACAATTGCGAAC
TGGCGTCTACTATCTATCAATGACAGCAGCTGGATTTTTAGTCTTTCTTTTAGCTCTCGT
GGTAGTAAGGTTCATACTATTTTGCACTATATGGATATGTACTGGCGGCAAGCATCACTT
CTGGTTCCTTCTTAATCTCA

>g6650.t19 Gene=g6650 Length=185
MTSKFAQGDNCLFPTRQIAIDYMDKMLAHKFFHRAKKIPVSEMELRGGRTKDKSKDQEKK
ETDAESSHEKDKSDKATSEKKKRKIRLEMHPQQIFIDGHEAYVWIYDPIPMTYWIFGALV
VIGAIVICLFPLWPPQLRTGVYYLSMTAAGFLVFLLALVVVRFILFCTIWICTGGKHHFW
FLLNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g6650.t19 MobiDBLite mobidb-lite consensus disorder prediction 43 83 -
2 g6650.t19 PANTHER PTHR12443:SF9 TRANSLOCATION PROTEIN SEC62 5 185 2.1E-54
3 g6650.t19 PANTHER PTHR12443 TRANSLOCATION PROTEIN SEC62 5 185 2.1E-54
1 g6650.t19 Pfam PF03839 Translocation protein Sec62 29 185 2.4E-50
7 g6650.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 112 -
10 g6650.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 134 -
9 g6650.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 139 -
11 g6650.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 172 -
8 g6650.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 173 185 -
4 g6650.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 134 -
5 g6650.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 144 166 -

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:0030176 integral component of endoplasmic reticulum membrane CC
GO:0015031 protein transport BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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