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.t9 TTS g6650.t9 17941016 17941016
chr_2 g6650 g6650.t9 isoform g6650.t9 17941126 17943095
chr_2 g6650 g6650.t9 exon g6650.t9.exon1 17941126 17941202
chr_2 g6650 g6650.t9 cds g6650.t9.CDS1 17941172 17941202
chr_2 g6650 g6650.t9 exon g6650.t9.exon2 17941275 17941504
chr_2 g6650 g6650.t9 cds g6650.t9.CDS2 17941275 17941504
chr_2 g6650 g6650.t9 exon g6650.t9.exon3 17941582 17942334
chr_2 g6650 g6650.t9 cds g6650.t9.CDS3 17941582 17942334
chr_2 g6650 g6650.t9 exon g6650.t9.exon4 17943054 17943095
chr_2 g6650 g6650.t9 cds g6650.t9.CDS4 17943054 17943095
chr_2 g6650 g6650.t9 TSS g6650.t9 17943212 17943212

Sequences

>g6650.t9 Gene=g6650 Length=1102
ATGTCGGGAAAAGATAAAAGAGTCAATAAAAAGAAAAAAGATGAATATAAAGAGAATGAT
GACGAGCAGGAAAAGGCAAGTAAAGAAGAGTATAAAGTTGCCAAGTGGATACGCAACAAT
GTTCCCGTGAAAAAAACTAAATTTCTCAATCACAATGTTGAATATTTTACATCAGCAAAA
GCGCTTGATGCTCTGATGACATCAAAATTCGCCCAAGGTGATAATTGTCTTTTTCCAACA
CGTCAAATTGCAATTGATTATATGGATAAAATGCTTGCACATAAATTTTTTCATCGTGCA
AAAAAGATACCTGTTAGTGAGATGGAATTGAGAGGTGGACGCACAAAAGACAAATCAAAA
GATCAAGAGAAAAAAGAAACAGATGCTGAAAGCTCACATGAGAAAGACAAAAGCGATAAA
GCAACATCAGAAAAGAAAAAAAGGAAAATTCGCTTGGAAATGCATCCACAACAGATTTTT
ATCGATGGACATGAAGCATATGTCTGGATTTATGATCCTATTCCGATGACTTATTGGATC
TTTGGAGCTCTTGTTGTAATTGGAGCAATAGTCATCTGTTTATTCCCACTCTGGCCACCA
CAATTGCGAACTGGCGTCTACTATCTATCAATGACAGCAGCTGGATTTTTAGTCTTTCTT
TTAGCTCTCGTGGTAGTAAGGTTCATACTATTTTGCACTATATGGATATGTACTGGCGGC
AAGCATCACTTCTGGTTCCTTCTTAATCTCACTGAAGATGTAGGTTTTATTGATTCATTT
AAACCACTCTATAAGCATGACTATATTGACAGTTCTGATACTAAAAATAAAAAAGATAAG
GACAAAAAGAAAAAGAAGAAGAAGGACAGTGATGACGAGAGTGGTAATAATAAGGAATCT
GAATTGGTCGATACAAAAGCTAAGGAGAGTGAAACAAATAATGAGGGCTCTATTTTGCAA
AGGAGAAAAACAAAAGCAAAAGAGCAAAATGAAGATATAATCAAAGATAATGAAGAAAGA
AAAAAAAAGCTCCGACTCACAAAGGTCATCAACTGATAAAGATTTTGAAATAGTGGATGC
AGAAGAAGACCATGAAGAATAA

>g6650.t9 Gene=g6650 Length=351
MSGKDKRVNKKKKDEYKENDDEQEKASKEEYKVAKWIRNNVPVKKTKFLNHNVEYFTSAK
ALDALMTSKFAQGDNCLFPTRQIAIDYMDKMLAHKFFHRAKKIPVSEMELRGGRTKDKSK
DQEKKETDAESSHEKDKSDKATSEKKKRKIRLEMHPQQIFIDGHEAYVWIYDPIPMTYWI
FGALVVIGAIVICLFPLWPPQLRTGVYYLSMTAAGFLVFLLALVVVRFILFCTIWICTGG
KHHFWFLLNLTEDVGFIDSFKPLYKHDYIDSSDTKNKKDKDKKKKKKKDSDDESGNNKES
ELVDTKAKESETNNEGSILQRRKTKAKEQNEDIIKDNEERKKKLRLTKVIN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g6650.t9 Coils Coil Coil 9 29 -
8 g6650.t9 MobiDBLite mobidb-lite consensus disorder prediction 1 29 -
6 g6650.t9 MobiDBLite mobidb-lite consensus disorder prediction 108 148 -
7 g6650.t9 MobiDBLite mobidb-lite consensus disorder prediction 275 351 -
9 g6650.t9 MobiDBLite mobidb-lite consensus disorder prediction 285 351 -
2 g6650.t9 PANTHER PTHR12443:SF9 TRANSLOCATION PROTEIN SEC62 15 333 9.1E-88
3 g6650.t9 PANTHER PTHR12443 TRANSLOCATION PROTEIN SEC62 15 333 9.1E-88
1 g6650.t9 Pfam PF03839 Translocation protein Sec62 94 287 3.8E-67
11 g6650.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 177 -
14 g6650.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 178 199 -
13 g6650.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 200 204 -
15 g6650.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 205 237 -
12 g6650.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 238 351 -
5 g6650.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 177 199 -
4 g6650.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 209 231 -

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