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.t7 TTS g6650.t7 17941016 17941016
chr_2 g6650 g6650.t7 isoform g6650.t7 17941126 17942524
chr_2 g6650 g6650.t7 exon g6650.t7.exon1 17941126 17941213
chr_2 g6650 g6650.t7 cds g6650.t7.CDS1 17941208 17941213
chr_2 g6650 g6650.t7 exon g6650.t7.exon2 17941283 17941504
chr_2 g6650 g6650.t7 cds g6650.t7.CDS2 17941283 17941504
chr_2 g6650 g6650.t7 exon g6650.t7.exon3 17941582 17942070
chr_2 g6650 g6650.t7 cds g6650.t7.CDS3 17941582 17942055
chr_2 g6650 g6650.t7 exon g6650.t7.exon4 17942160 17942334
chr_2 g6650 g6650.t7 exon g6650.t7.exon5 17942430 17942524
chr_2 g6650 g6650.t7 TSS g6650.t7 17943212 17943212

Sequences

>g6650.t7 Gene=g6650 Length=1069
GCTCCTATTTAAATTAATCTTATTTTTTTATCTTATTTGAGCTTGTATTTATAAATTTCT
TTAAATATTAACAACCATATGAAATGACATTTTATGAATATAAAGAGAATGATGACGAGC
AGGAAAAGGCAAGTAAAGAAGAGTATAAAGTTGCCAAGTGGATACGCAACAATGTTCCCG
TGAAAAAAACTAAATTTCTCAATCACAATGTTGAATATTTTACATCAGCAAAAGCGCTTG
ATGCTCTGATGACATCAAAATTCGCCCAAGATACCTGTTAGTGAGATGGAATTGAGAGGT
GGACGCACAAAAGACAAATCAAAAGATCAAGAGAAAAAAGAAACAGATGCTGAAAGCTCA
CATGAGAAAGACAAAAGCGATAAAGCAACATCAGAAAAGAAAAAAAGGAAAATTCGCTTG
GAAATGCATCCACAACAGATTTTTATCGATGGACATGAAGCATATGTCTGGATTTATGAT
CCTATTCCGATGACTTATTGGATCTTTGGAGCTCTTGTTGTAATTGGAGCAATAGTCATC
TGTTTATTCCCACTCTGGCCACCACAATTGCGAACTGGCGTCTACTATCTATCAATGACA
GCAGCTGGATTTTTAGTCTTTCTTTTAGCTCTCGTGGTAGTAAGGTTCATACTATTTTGC
ACTATATGGATATGTACTGGCGGCAAGCATCACTTCTGGTTCCTTCTTAATCTCACTGAA
GATGTAGGTTTTATTGATTCATTTAAACCACTCTATAAGCATGACTATATTGACAGTTCT
GATACTAAAAATAAAAAAGATAAGGACAAAAAGAAAAAGAAGAAGAAGGACAGTGATGAC
GAGAGTGGTAATAATAAGGAATCTGAATTGGTCGATACAAAAGCTAAGGAGAGTGAAACA
AATAATGAGGGCTCTATTTTGCAAAGGAGAAAAACAAAAGCAAAAGAGCAAAATGAAGAT
ATAATCAAAGATAATGAAGAATTCTGAGTCAGAAAGCTCCGACTCACAAAGGTCATCAAC
TGATAAAGATTTTGAAATAGTGGATGCAGAAGAAGACCATGAAGAATAA

>g6650.t7 Gene=g6650 Length=233
MELRGGRTKDKSKDQEKKETDAESSHEKDKSDKATSEKKKRKIRLEMHPQQIFIDGHEAY
VWIYDPIPMTYWIFGALVVIGAIVICLFPLWPPQLRTGVYYLSMTAAGFLVFLLALVVVR
FILFCTIWICTGGKHHFWFLLNLTEDVGFIDSFKPLYKHDYIDSSDTKNKKDKDKKKKKK
KDSDDESGNNKESELVDTKAKESETNNEGSILQRRKTKAKEQNEDIIKDNEEF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g6650.t7 MobiDBLite mobidb-lite consensus disorder prediction 1 41 -
6 g6650.t7 MobiDBLite mobidb-lite consensus disorder prediction 168 233 -
7 g6650.t7 MobiDBLite mobidb-lite consensus disorder prediction 178 233 -
2 g6650.t7 PANTHER PTHR12443:SF9 TRANSLOCATION PROTEIN SEC62 30 219 3.9E-63
3 g6650.t7 PANTHER PTHR12443 TRANSLOCATION PROTEIN SEC62 30 219 3.9E-63
1 g6650.t7 Pfam PF03839 Translocation protein Sec62 13 180 4.4E-69
10 g6650.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 70 -
12 g6650.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 71 92 -
11 g6650.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 93 97 -
13 g6650.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 98 130 -
9 g6650.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 131 233 -
5 g6650.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 70 92 -
4 g6650.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 102 124 -

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

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