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.t4 TTS g6650.t4 17941016 17941016
chr_2 g6650 g6650.t4 isoform g6650.t4 17941126 17942334
chr_2 g6650 g6650.t4 exon g6650.t4.exon1 17941126 17941213
chr_2 g6650 g6650.t4 cds g6650.t4.CDS1 17941126 17941213
chr_2 g6650 g6650.t4 exon g6650.t4.exon2 17941275 17941504
chr_2 g6650 g6650.t4 cds g6650.t4.CDS2 17941275 17941504
chr_2 g6650 g6650.t4 exon g6650.t4.exon3 17941582 17942334
chr_2 g6650 g6650.t4 cds g6650.t4.CDS3 17941582 17942181
chr_2 g6650 g6650.t4 TSS g6650.t4 17943212 17943212

Sequences

>g6650.t4 Gene=g6650 Length=1071
GAATATAAAGAGAATGATGACGAGCAGGAAAAGGCAAGTAAAGAAGAGTATAAAGTTGCC
AAGTGGATACGCAACAATGTTCCCGTGAAAAAAACTAAATTTCTCAATCACAATGTTGAA
TATTTTACATCAGCAAAAGCGCTTGATGCTCTGATGACATCAAAATTCGCCCAAGGTGAT
AATTGTCTTTTTCCAACACGTCAAATTGCAATTGATTATATGGATAAAATGCTTGCACAT
AAATTTTTTCATCGTGCAAAAAAGATACCTGTTAGTGAGATGGAATTGAGAGGTGGACGC
ACAAAAGACAAATCAAAAGATCAAGAGAAAAAAGAAACAGATGCTGAAAGCTCACATGAG
AAAGACAAAAGCGATAAAGCAACATCAGAAAAGAAAAAAAGGAAAATTCGCTTGGAAATG
CATCCACAACAGATTTTTATCGATGGACATGAAGCATATGTCTGGATTTATGATCCTATT
CCGATGACTTATTGGATCTTTGGAGCTCTTGTTGTAATTGGAGCAATAGTCATCTGTTTA
TTCCCACTCTGGCCACCACAATTGCGAACTGGCGTCTACTATCTATCAATGACAGCAGCT
GGATTTTTAGTCTTTCTTTTAGCTCTCGTGGTAGTAAGGTTCATACTATTTTGCACTATA
TGGATATGTACTGGCGGCAAGCATCACTTCTGGTTCCTTCTTAATCTCACTGAAGATGTA
GGTTTTATTGATTCATTTAAACCACTCTATAAGCATGACTATATTGACAGTTCTGATACT
AAAAATAAAAAAGATAAGGACAAAAAGAAAAAGAAGAAGAAGGACAGTGATGACGAGAGT
GGTAATAATAAGGAATCTGAATTGGTCGATACAAAAGCTAAGGAGAGTGAAACAAATAAT
GAGGGCTCTATTTTGCAAAGGAGAAAAACAAAAGCAAAAGAGCAAAATGAAGATATAATC
AAAGATAATGAAGAAAGAAAAAATTCTGAGTCAGAAAGCTCCGACTCACAAAGGTCATCA
ACTGATAAAGATTTTGAAATAGTGGATGCAGAAGAAGACCATGAAGAATAA

>g6650.t4 Gene=g6650 Length=305
MTSKFAQGDNCLFPTRQIAIDYMDKMLAHKFFHRAKKIPVSEMELRGGRTKDKSKDQEKK
ETDAESSHEKDKSDKATSEKKKRKIRLEMHPQQIFIDGHEAYVWIYDPIPMTYWIFGALV
VIGAIVICLFPLWPPQLRTGVYYLSMTAAGFLVFLLALVVVRFILFCTIWICTGGKHHFW
FLLNLTEDVGFIDSFKPLYKHDYIDSSDTKNKKDKDKKKKKKKDSDDESGNNKESELVDT
KAKESETNNEGSILQRRKTKAKEQNEDIIKDNEERKNSESESSDSQRSSTDKDFEIVDAE
EDHEE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6650.t4 Coils Coil Coil 261 281 -
7 g6650.t4 MobiDBLite mobidb-lite consensus disorder prediction 43 83 -
8 g6650.t4 MobiDBLite mobidb-lite consensus disorder prediction 210 305 -
6 g6650.t4 MobiDBLite mobidb-lite consensus disorder prediction 220 296 -
2 g6650.t4 PANTHER PTHR12443:SF9 TRANSLOCATION PROTEIN SEC62 5 304 2.2E-76
3 g6650.t4 PANTHER PTHR12443 TRANSLOCATION PROTEIN SEC62 5 304 2.2E-76
1 g6650.t4 Pfam PF03839 Translocation protein Sec62 29 222 8.6E-68
10 g6650.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 112 -
13 g6650.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 134 -
12 g6650.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 139 -
14 g6650.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 172 -
11 g6650.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 173 305 -
4 g6650.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 134 -
5 g6650.t4 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

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