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.t5 isoform g14212.t5 35445302 35447128
chr_1 g14212 g14212.t5 exon g14212.t5.exon1 35445302 35446385
chr_1 g14212 g14212.t5 cds g14212.t5.CDS1 35445873 35446385
chr_1 g14212 g14212.t5 exon g14212.t5.exon2 35446458 35446639
chr_1 g14212 g14212.t5 cds g14212.t5.CDS2 35446458 35446639
chr_1 g14212 g14212.t5 exon g14212.t5.exon3 35446709 35446861
chr_1 g14212 g14212.t5 cds g14212.t5.CDS3 35446709 35446861
chr_1 g14212 g14212.t5 exon g14212.t5.exon4 35446944 35447128
chr_1 g14212 g14212.t5 cds g14212.t5.CDS4 35446944 35447097
chr_1 g14212 g14212.t5 TSS g14212.t5 35447866 35447866
chr_1 g14212 g14212.t5 TTS g14212.t5 NA NA

Sequences

>g14212.t5 Gene=g14212 Length=1604
ACTTTTTAACGGCGCACAGAAACTCTTTGGCATGGTCATCACAATTGGTCAGGCAATTGT
ATACGTAATGACAGGAATGTATGGTGATCCAGCAGAAATTGGTGCCGGTGTCTGTCTACT
CATCATCATTCAACTCTTTGTTGCTGGTCTTATCGTTCTTTTGCTCGATGAGTTACTTCA
AAAAGGTTACGGTTTGGGTTCTGGAATTTCACTTTTCATTGCAACGAACATTTGTGAGAC
AATCGTATGGAAAGCATTTTCACCTGCAACTGTTAACACTGGTCGTGGTACAGAATTCGA
GGGCGCTGTAATTGCACTGTTCCATCTTCTTGCAACACTTGCTACCGTACTCGTCTTTGC
TATAGTTATATACTTCCAAGGATTCCGTGTCGATTTGCCAATCAAATCAGCTCGCTATCG
CGGTCAATACAGCAGTTATCCAATCAAACTTTTCTATACATCAAACATTCCCATCATCTT
GCAATCGGCACTTGTTTCAAATCTTTACGTTATTTCACAGATGCTTGCTGTTAAATTTCA
TGGAAACTTCCTTGTAAACCTATTAGGAGTTTGGGCTGATGTCGGTGGTGGCGGTCCAGC
AAGATCATACCCTATTGGAGGTTTATGCTACTATTTTTCACCACCAGAAAGTCTTGGTCA
CATCTTGCAAGATCCAGTTCATGCAGTTCTCTATATTATTTTTATGCTCGGTTCATGCGC
TTTCTTCTCAAAAACGTGGATTGATGTTTCAGGAAGCTCTGCCAAGGATGTTGCAAAACA
ATTGAAAGAACAACAAATGGTTATGCGTGGACATCGTGAAAACTCAATGATTCATGAGTT
GAATCGTTACATCCCAACTGCAGCTGCTTTCGGTGGTCTCTGCATTGGTGCACTCTCAGT
AATGGCTGATTTCCTCGGAGCTATTGGTTCAGGAACTGGTATCCTTCTCGCTGTAACAAT
CATCTATCAGTACTTTGAAATCTTTGTGAAGGAACAAAGTGAAGGTTTAGGAATGGGCAG
TTTACTGTTTTAAAAAATCTGCATGCAGCATTTAGCATTATCAACATACTCCTCCTCCTC
TCCCCTCTCACATTTTACATAAACAAAAAATCATACACATACACACATAAAAAGAAATTT
AAAAGGTGGATGAATATCACTAAGATTGATTACTTATTATTTCTTCCGTCACTAATAAAC
ACCTTCGATTTAAATGAAGAAATATAATAAAAATTTTATAATATAAAAGAGAAAAAGAAT
GAAGAGAAATATAGACAATGTTTTTTTTTAAAAGAGAGAATTAACATCTTATGTTCTTAA
AATTGCAATAATTTTTAATTTTCTTTCATCCCATTTTATAAAATCTATTTTTTATTTGAA
AAAAAAAAACTTCGTGTGTCGTATTTAATAAGACATTTTTTCATGATTTGATAGAAATAT
TAAAATGAAGATCATGAATGTGAGAAATAAGAAAATATAATTTAAGTAAAATGTTGTAAA
AGTTAATTAAACGAATAAAGATGATGAAAAAACTGAAATGATTTTCAATAGAAGAAAAGA
TTTGTTTTATTTTTATTTTCATACGATATCATTTTTGAATATTT

>g14212.t5 Gene=g14212 Length=333
MVITIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATLATVLVFAIVIYFQGFRV
DLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLYVISQMLAVKFHGNFLVNLLGV
WADVGGGGPARSYPIGGLCYYFSPPESLGHILQDPVHAVLYIIFMLGSCAFFSKTWIDVS
GSSAKDVAKQLKEQQMVMRGHRENSMIHELNRYIPTAAAFGGLCIGALSVMADFLGAIGS
GTGILLAVTIIYQYFEIFVKEQSEGLGMGSLLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g14212.t5 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 1 330 1.2E-122
3 g14212.t5 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 1 102 8.6E-202
5 g14212.t5 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 1 102 8.6E-202
2 g14212.t5 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 103 332 8.6E-202
4 g14212.t5 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 103 332 8.6E-202
1 g14212.t5 Pfam PF00344 SecY translocase 1 314 5.7E-60
14 g14212.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 22 -
19 g14212.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 23 45 -
9 g14212.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 46 51 -
18 g14212.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 73 -
12 g14212.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 74 92 -
20 g14212.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
8 g14212.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 116 135 -
22 g14212.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 161 -
13 g14212.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 162 217 -
16 g14212.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 237 -
11 g14212.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 238 269 -
21 g14212.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 270 288 -
15 g14212.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 289 293 -
17 g14212.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 294 315 -
10 g14212.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 316 333 -
30 g14212.t5 ProSitePatterns PS00756 Protein secY signature 2. 44 62 -
6 g14212.t5 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 2 321 3.79E-84
31 g14212.t5 TIGRFAM TIGR00967 3a0501s007: preprotein translocase, SecY subunit 1 322 5.1E-83
25 g14212.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 23 45 -
24 g14212.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 73 -
26 g14212.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
23 g14212.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
29 g14212.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 215 237 -
27 g14212.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 270 292 -
28 g14212.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 297 319 -

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