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.t16 isoform g14212.t16 35446942 35447733
chr_1 g14212 g14212.t16 exon g14212.t16.exon1 35446942 35447382
chr_1 g14212 g14212.t16 cds g14212.t16.CDS1 35446942 35447382
chr_1 g14212 g14212.t16 exon g14212.t16.exon2 35447494 35447561
chr_1 g14212 g14212.t16 cds g14212.t16.CDS2 35447494 35447561
chr_1 g14212 g14212.t16 exon g14212.t16.exon3 35447727 35447733
chr_1 g14212 g14212.t16 cds g14212.t16.CDS3 35447727 35447733
chr_1 g14212 g14212.t16 TSS g14212.t16 35447866 35447866
chr_1 g14212 g14212.t16 TTS g14212.t16 NA NA

Sequences

>g14212.t16 Gene=g14212 Length=516
ATGGGAATTAAATTCCTGGAAGTTATAAAACCATTTTGCAGCATTCTGCCGGAAGTAACG
AAGCCAGAACGAAAGATCCAATTTCGTGAAAAAGTGCTATGGACCGCAATAACTTTATTC
ATTTTCCTGGTATGTTGTCAAATTCCACTATTCGGTATAATGTCATCAGATTCAGCCGAT
CCTTTCTATTGGATTCGTGTTATTCTCGCTTCTAATCGTGGTACTTTAATGGAATTGGGT
ATTTCCCCAATTGTCACATCTGGTCTCATTATGCAATTACTTGCTGGTGTTAAAATTATT
GAAGTCGGTGATACACCAAAAGACAGGGCACTTTTTAACGGCGCACAGAAACTCTTTGGC
ATGGTCATCACAATTGGTCAGGCAATTGTATACGTAATGACAGGAATGTATGGTGATCCA
GCAGAAATTGGTGCCGGTGTCTGTCTACTCATCATCATTCAACTCTTTGTTGCTGGTCTT
ATCGTTCTTTTGCTCGATGAGTTACTTCAAAAAGGT

>g14212.t16 Gene=g14212 Length=172
MGIKFLEVIKPFCSILPEVTKPERKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGVKIIEVGDTPKDRALFNGAQKLFG
MVITIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14212.t16 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 6 172 2.7E-64
3 g14212.t16 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 1 172 5.9E-108
4 g14212.t16 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 1 172 5.9E-108
1 g14212.t16 Pfam PF10559 Plug domain of Sec61p 40 74 1.9E-17
2 g14212.t16 Pfam PF00344 SecY translocase 75 171 8.6E-20
13 g14212.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 31 -
17 g14212.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 54 -
16 g14212.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 55 73 -
18 g14212.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 97 -
14 g14212.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 98 117 -
20 g14212.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 137 -
15 g14212.t16 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 138 142 -
19 g14212.t16 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
12 g14212.t16 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 166 172 -
10 g14212.t16 ProSitePatterns PS00755 Protein secY signature 1. 75 94 -
9 g14212.t16 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 8 171 4.45E-45
8 g14212.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -
5 g14212.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 75 97 -
6 g14212.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 138 -
7 g14212.t16 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -

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