Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein transport protein Sec61 subunit alpha isoform 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_1 g14212 g14212.t4 isoform g14212.t4 35445302 35447128
chr_1 g14212 g14212.t4 exon g14212.t4.exon1 35445302 35446385
chr_1 g14212 g14212.t4 cds g14212.t4.CDS1 35445873 35446385
chr_1 g14212 g14212.t4 exon g14212.t4.exon2 35446458 35446861
chr_1 g14212 g14212.t4 cds g14212.t4.CDS2 35446458 35446861
chr_1 g14212 g14212.t4 exon g14212.t4.exon3 35446944 35447128
chr_1 g14212 g14212.t4 cds g14212.t4.CDS3 35446944 35447097
chr_1 g14212 g14212.t4 TSS g14212.t4 35447866 35447866
chr_1 g14212 g14212.t4 TTS g14212.t4 NA NA

Sequences

>g14212.t4 Gene=g14212 Length=1673
ACTTTTTAACGGCGCACAGAAACTCTTTGGCATGGTCATCACAATTGGTCAGGCAATTGT
ATACGTAATGACAGGAATGTATGGTGATCCAGCAGAAATTGGTGCCGGTGTCTGTCTACT
CATCATCATTCAACTCTTTGTTGCTGGTCTTATCGTTCTTTTGCTCGATGAGTTACTTCA
AAAAGGTTACGGTTTGGGTTCTGGAATTTCACTTTTCATTGCAACGAACATTTGTGAGAC
AATCGTATGGAAAGCATTTTCACCTGCAACTGTTAACACTGGTCGTGGTACAGAATTCGA
GGGCGCTGTAATTGCACTGTTCCATCTTCTTGCAACACGTCAAGACAAAGTTCGTGGTTT
ACGAGAGGCTTTTTATCGTCAAAATTTGCCCAATTTAATGAACTTGCTTGCTACCGTACT
CGTCTTTGCTATAGTTATATACTTCCAAGGATTCCGTGTCGATTTGCCAATCAAATCAGC
TCGCTATCGCGGTCAATACAGCAGTTATCCAATCAAACTTTTCTATACATCAAACATTCC
CATCATCTTGCAATCGGCACTTGTTTCAAATCTTTACGTTATTTCACAGATGCTTGCTGT
TAAATTTCATGGAAACTTCCTTGTAAACCTATTAGGAGTTTGGGCTGATGTCGGTGGTGG
CGGTCCAGCAAGATCATACCCTATTGGAGGTTTATGCTACTATTTTTCACCACCAGAAAG
TCTTGGTCACATCTTGCAAGATCCAGTTCATGCAGTTCTCTATATTATTTTTATGCTCGG
TTCATGCGCTTTCTTCTCAAAAACGTGGATTGATGTTTCAGGAAGCTCTGCCAAGGATGT
TGCAAAACAATTGAAAGAACAACAAATGGTTATGCGTGGACATCGTGAAAACTCAATGAT
TCATGAGTTGAATCGTTACATCCCAACTGCAGCTGCTTTCGGTGGTCTCTGCATTGGTGC
ACTCTCAGTAATGGCTGATTTCCTCGGAGCTATTGGTTCAGGAACTGGTATCCTTCTCGC
TGTAACAATCATCTATCAGTACTTTGAAATCTTTGTGAAGGAACAAAGTGAAGGTTTAGG
AATGGGCAGTTTACTGTTTTAAAAAATCTGCATGCAGCATTTAGCATTATCAACATACTC
CTCCTCCTCTCCCCTCTCACATTTTACATAAACAAAAAATCATACACATACACACATAAA
AAGAAATTTAAAAGGTGGATGAATATCACTAAGATTGATTACTTATTATTTCTTCCGTCA
CTAATAAACACCTTCGATTTAAATGAAGAAATATAATAAAAATTTTATAATATAAAAGAG
AAAAAGAATGAAGAGAAATATAGACAATGTTTTTTTTTAAAAGAGAGAATTAACATCTTA
TGTTCTTAAAATTGCAATAATTTTTAATTTTCTTTCATCCCATTTTATAAAATCTATTTT
TTATTTGAAAAAAAAAAACTTCGTGTGTCGTATTTAATAAGACATTTTTTCATGATTTGA
TAGAAATATTAAAATGAAGATCATGAATGTGAGAAATAAGAAAATATAATTTAAGTAAAA
TGTTGTAAAAGTTAATTAAACGAATAAAGATGATGAAAAAACTGAAATGATTTTCAATAG
AAGAAAAGATTTGTTTTATTTTTATTTTCATACGATATCATTTTTGAATATTT

>g14212.t4 Gene=g14212 Length=356
MVITIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRGLREAFYRQNLP
NLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSN
LYVISQMLAVKFHGNFLVNLLGVWADVGGGGPARSYPIGGLCYYFSPPESLGHILQDPVH
AVLYIIFMLGSCAFFSKTWIDVSGSSAKDVAKQLKEQQMVMRGHRENSMIHELNRYIPTA
AAFGGLCIGALSVMADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEGLGMGSLLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g14212.t4 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 1 353 1.3E-138
2 g14212.t4 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 1 355 7.4E-227
3 g14212.t4 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 1 355 7.4E-227
1 g14212.t4 Pfam PF00344 SecY translocase 1 337 1.1E-61
13 g14212.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 22 -
19 g14212.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 23 45 -
7 g14212.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 46 51 -
18 g14212.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 73 -
12 g14212.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 74 121 -
17 g14212.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 122 143 -
6 g14212.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 144 162 -
20 g14212.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 163 184 -
10 g14212.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 185 240 -
16 g14212.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 241 260 -
8 g14212.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 261 292 -
15 g14212.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 293 311 -
11 g14212.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 312 316 -
14 g14212.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 317 338 -
9 g14212.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 339 356 -
29 g14212.t4 ProSitePatterns PS00756 Protein secY signature 2. 44 62 -
4 g14212.t4 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 2 344 1.01E-86
30 g14212.t4 TIGRFAM TIGR00967 3a0501s007: preprotein translocase, SecY subunit 1 345 3.5E-88
25 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 23 45 -
21 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
26 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 119 141 -
24 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 161 183 -
27 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 196 218 -
23 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 238 260 -
22 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 293 315 -
28 g14212.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 320 342 -

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:0016020 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.

Raw TPM values