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.t14 TTS g14212.t14 35445637 35445637
chr_1 g14212 g14212.t14 isoform g14212.t14 35446501 35447733
chr_1 g14212 g14212.t14 exon g14212.t14.exon1 35446501 35446861
chr_1 g14212 g14212.t14 cds g14212.t14.CDS1 35446503 35446861
chr_1 g14212 g14212.t14 exon g14212.t14.exon2 35446944 35447382
chr_1 g14212 g14212.t14 cds g14212.t14.CDS2 35446944 35447382
chr_1 g14212 g14212.t14 exon g14212.t14.exon3 35447494 35447561
chr_1 g14212 g14212.t14 cds g14212.t14.CDS3 35447494 35447561
chr_1 g14212 g14212.t14 exon g14212.t14.exon4 35447727 35447733
chr_1 g14212 g14212.t14 cds g14212.t14.CDS4 35447727 35447733
chr_1 g14212 g14212.t14 TSS g14212.t14 35447866 35447866

Sequences

>g14212.t14 Gene=g14212 Length=875
ATGGGAATTAAATTCCTGGAAGTTATAAAACCATTTTGCAGCATTCTGCCGGAAGTAACG
AAGCCAGAACGAAAGATCCAATTTCGTGAAAAAGTGCTATGGACCGCAATAACTTTATTC
ATTTTCCTGGTATGTTGTCAAATTCCACTATTCGGTATAATGTCATCAGATTCAGCCGAT
CCTTTCTATTGGATTCGTGTTATTCTCGCTTCTAATCGTGGTACTTTAATGGAATTGGGT
ATTTCCCCAATTGTCACATCTGGTCTCATTATGCAATTACTTGCTGGTGTTAAAATTATT
GAAGTCGGTGATACACCAAAAGACAGGGCACTTTTTAACGGCGCACAGAAACTCTTTGGC
ATGGTCATCACAATTGGTCAGGCAATTGTATACGTAATGACAGGAATGTATGGTGATCCA
GCAGAAATTGGTGCCGGTGTCTGTCTACTCATCATCATTCAACTCTTTGTTGCTGGTCTT
ATCGTTCTTTTGCTCGATGAGTTACTTCAAAAAGGTTACGGTTTGGGTTCTGGAATTTCA
CTTTTCATTGCAACGAACATTTGTGAGACAATCGTATGGAAAGCATTTTCACCTGCAACT
GTTAACACTGGTCGTGGTACAGAATTCGAGGGCGCTGTAATTGCACTGTTCCATCTTCTT
GCAACACGTCAAGACAAAGTTCGTGGTTTACGAGAGGCTTTTTATCGTCAAAATTTGCCC
AATTTAATGAACTTGCTTGCTACCGTACTCGTCTTTGCTATAGTTATATACTTCCAAGGA
TTCCGTGTCGATTTGCCAATCAAATCAGCTCGCTATCGCGGTCAATACAGCAGTTATCCA
ATCAAACTTTTCTATACATCAAACATTCCCATCAT

>g14212.t14 Gene=g14212 Length=291
MGIKFLEVIKPFCSILPEVTKPERKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGVKIIEVGDTPKDRALFNGAQKLFG
MVITIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRGLREAFYRQNLP
NLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g14212.t14 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 28 291 8.7E-109
3 g14212.t14 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 1 291 6.8E-193
4 g14212.t14 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 1 291 6.8E-193
1 g14212.t14 Pfam PF10559 Plug domain of Sec61p 40 74 4.2E-17
2 g14212.t14 Pfam PF00344 SecY translocase 75 291 3.7E-46
8 g14212.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 31 -
15 g14212.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 54 -
13 g14212.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 55 73 -
17 g14212.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 97 -
9 g14212.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 98 117 -
19 g14212.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 137 -
12 g14212.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 138 142 -
18 g14212.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
7 g14212.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 166 171 -
16 g14212.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 193 -
11 g14212.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 194 241 -
14 g14212.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 242 261 -
10 g14212.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 262 291 -
27 g14212.t14 ProSitePatterns PS00755 Protein secY signature 1. 75 94 -
26 g14212.t14 ProSitePatterns PS00756 Protein secY signature 2. 164 182 -
5 g14212.t14 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 8 291 3.53E-76
28 g14212.t14 TIGRFAM TIGR00967 3a0501s007: preprotein translocase, SecY subunit 29 291 4.2E-77
25 g14212.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -
20 g14212.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 75 97 -
22 g14212.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 138 -
24 g14212.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
21 g14212.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 172 193 -
23 g14212.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 239 261 -

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

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