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.t3 isoform g14212.t3 35445302 35446856
chr_1 g14212 g14212.t3 exon g14212.t3.exon1 35445302 35446385
chr_1 g14212 g14212.t3 cds g14212.t3.CDS1 35445873 35446385
chr_1 g14212 g14212.t3 exon g14212.t3.exon2 35446458 35446856
chr_1 g14212 g14212.t3 cds g14212.t3.CDS2 35446458 35446649
chr_1 g14212 g14212.t3 TSS g14212.t3 35447866 35447866
chr_1 g14212 g14212.t3 TTS g14212.t3 NA NA

Sequences

>g14212.t3 Gene=g14212 Length=1483
GGTTTGGGTTCTGGAATTTCACTTTTCATTGCAACGAACATTTGTGAGACAATCGTATGG
AAAGCATTTTCACCTGCAACTGTTAACACTGGTCGTGGTACAGAATTCGAGGGCGCTGTA
ATTGCACTGTTCCATCTTCTTGCAACACGTCAAGACAAAGTTCGTGGTTTACGAGAGGCT
TTTTATCGTCAAAATTTGCCCAATTTAATGAACTTGCTTGCTACCGTACTCGTCTTTGCT
ATAGTTATATACTTCCAAGGATTCCGTGTCGATTTGCCAATCAAATCAGCTCGCTATCGC
GGTCAATACAGCAGTTATCCAATCAAACTTTTCTATACATCAAACATTCCCATCATCTTG
CAATCGGCACTTGTTTCAAATCTTTACGTTATTTCACAGATGCTTGCTGTTAAATTTCAT
GGAAACTTCCTTGTAAACCTATTAGGAGTTTGGGCTGATGTCGGTGGTGGCGGTCCAGCA
AGATCATACCCTATTGGAGGTTTATGCTACTATTTTTCACCACCAGAAAGTCTTGGTCAC
ATCTTGCAAGATCCAGTTCATGCAGTTCTCTATATTATTTTTATGCTCGGTTCATGCGCT
TTCTTCTCAAAAACGTGGATTGATGTTTCAGGAAGCTCTGCCAAGGATGTTGCAAAACAA
TTGAAAGAACAACAAATGGTTATGCGTGGACATCGTGAAAACTCAATGATTCATGAGTTG
AATCGTTACATCCCAACTGCAGCTGCTTTCGGTGGTCTCTGCATTGGTGCACTCTCAGTA
ATGGCTGATTTCCTCGGAGCTATTGGTTCAGGAACTGGTATCCTTCTCGCTGTAACAATC
ATCTATCAGTACTTTGAAATCTTTGTGAAGGAACAAAGTGAAGGTTTAGGAATGGGCAGT
TTACTGTTTTAAAAAATCTGCATGCAGCATTTAGCATTATCAACATACTCCTCCTCCTCT
CCCCTCTCACATTTTACATAAACAAAAAATCATACACATACACACATAAAAAGAAATTTA
AAAGGTGGATGAATATCACTAAGATTGATTACTTATTATTTCTTCCGTCACTAATAAACA
CCTTCGATTTAAATGAAGAAATATAATAAAAATTTTATAATATAAAAGAGAAAAAGAATG
AAGAGAAATATAGACAATGTTTTTTTTTAAAAGAGAGAATTAACATCTTATGTTCTTAAA
ATTGCAATAATTTTTAATTTTCTTTCATCCCATTTTATAAAATCTATTTTTTATTTGAAA
AAAAAAAACTTCGTGTGTCGTATTTAATAAGACATTTTTTCATGATTTGATAGAAATATT
AAAATGAAGATCATGAATGTGAGAAATAAGAAAATATAATTTAAGTAAAATGTTGTAAAA
GTTAATTAAACGAATAAAGATGATGAAAAAACTGAAATGATTTTCAATAGAAGAAAAGAT
TTGTTTTATTTTTATTTTCATACGATATCATTTTTGAATATTT

>g14212.t3 Gene=g14212 Length=234
MNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLY
VISQMLAVKFHGNFLVNLLGVWADVGGGGPARSYPIGGLCYYFSPPESLGHILQDPVHAV
LYIIFMLGSCAFFSKTWIDVSGSSAKDVAKQLKEQQMVMRGHRENSMIHELNRYIPTAAA
FGGLCIGALSVMADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEGLGMGSLLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14212.t3 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 1 231 2.3E-93
2 g14212.t3 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 1 233 2.6E-142
3 g14212.t3 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 1 233 2.6E-142
1 g14212.t3 Pfam PF00344 SecY translocase 2 215 1.6E-41
18 g14212.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
19 g14212.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
20 g14212.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
26 g14212.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 18 -
16 g14212.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 41 -
21 g14212.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 42 62 -
14 g14212.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 63 73 -
22 g14212.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 96 -
17 g14212.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 97 115 -
23 g14212.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 134 -
12 g14212.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 135 170 -
25 g14212.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 189 -
15 g14212.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 190 194 -
24 g14212.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 195 216 -
13 g14212.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 217 234 -
10 g14212.t3 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 2 222 1.02E-61
9 g14212.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 19 -
5 g14212.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 61 -
7 g14212.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 74 96 -
8 g14212.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 116 138 -
4 g14212.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 171 193 -
6 g14212.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 198 220 -

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