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.t11 TTS g14212.t11 35445352 35445352
chr_1 g14212 g14212.t11 isoform g14212.t11 35445873 35447733
chr_1 g14212 g14212.t11 exon g14212.t11.exon1 35445873 35446385
chr_1 g14212 g14212.t11 cds g14212.t11.CDS1 35445873 35446385
chr_1 g14212 g14212.t11 exon g14212.t11.exon2 35446470 35446861
chr_1 g14212 g14212.t11 cds g14212.t11.CDS2 35446470 35446861
chr_1 g14212 g14212.t11 exon g14212.t11.exon3 35446944 35447382
chr_1 g14212 g14212.t11 cds g14212.t11.CDS3 35446944 35447382
chr_1 g14212 g14212.t11 exon g14212.t11.exon4 35447494 35447561
chr_1 g14212 g14212.t11 cds g14212.t11.CDS4 35447494 35447561
chr_1 g14212 g14212.t11 exon g14212.t11.exon5 35447727 35447733
chr_1 g14212 g14212.t11 cds g14212.t11.CDS5 35447727 35447733
chr_1 g14212 g14212.t11 TSS g14212.t11 35447866 35447866

Sequences

>g14212.t11 Gene=g14212 Length=1419
ATGGGAATTAAATTCCTGGAAGTTATAAAACCATTTTGCAGCATTCTGCCGGAAGTAACG
AAGCCAGAACGAAAGATCCAATTTCGTGAAAAAGTGCTATGGACCGCAATAACTTTATTC
ATTTTCCTGGTATGTTGTCAAATTCCACTATTCGGTATAATGTCATCAGATTCAGCCGAT
CCTTTCTATTGGATTCGTGTTATTCTCGCTTCTAATCGTGGTACTTTAATGGAATTGGGT
ATTTCCCCAATTGTCACATCTGGTCTCATTATGCAATTACTTGCTGGTGTTAAAATTATT
GAAGTCGGTGATACACCAAAAGACAGGGCACTTTTTAACGGCGCACAGAAACTCTTTGGC
ATGGTCATCACAATTGGTCAGGCAATTGTATACGTAATGACAGGAATGTATGGTGATCCA
GCAGAAATTGGTGCCGGTGTCTGTCTACTCATCATCATTCAACTCTTTGTTGCTGGTCTT
ATCGTTCTTTTGCTCGATGAGTTACTTCAAAAAGGTTACGGTTTGGGTTCTGGAATTTCA
CTTTTCATTGCAACGAACATTTGTGAGACAATCGTATGGAAAGCATTTTCACCTGCAACT
GTTAACACTGGTCGTGGTACAGAATTCGAGGGCGCTGTAATTGCACTGTTCCATCTTCTT
GCAACACGTCAAGACAAAGTTCGTGGTTTACGAGAGGCTTTTTATCGTCAAAATTTGCCC
AATTTAATGAACTTGCTTGCTACCGTACTCGTCTTTGCTATAGTTATATACTTCCAAGGA
TTCCGTGTCGATTTGCCAATCAAATCAGCTCGCTATCGCGGTCAATACAGCAGTTATCCA
ATCAAACTTTTCTATACATCAAACATTCCCATCATCTTGCAATCGGCACTTGTTTCAAAT
CTTTACATGCTTGCTGTTAAATTTCATGGAAACTTCCTTGTAAACCTATTAGGAGTTTGG
GCTGATGTCGGTGGTGGCGGTCCAGCAAGATCATACCCTATTGGAGGTTTATGCTACTAT
TTTTCACCACCAGAAAGTCTTGGTCACATCTTGCAAGATCCAGTTCATGCAGTTCTCTAT
ATTATTTTTATGCTCGGTTCATGCGCTTTCTTCTCAAAAACGTGGATTGATGTTTCAGGA
AGCTCTGCCAAGGATGTTGCAAAACAATTGAAAGAACAACAAATGGTTATGCGTGGACAT
CGTGAAAACTCAATGATTCATGAGTTGAATCGTTACATCCCAACTGCAGCTGCTTTCGGT
GGTCTCTGCATTGGTGCACTCTCAGTAATGGCTGATTTCCTCGGAGCTATTGGTTCAGGA
ACTGGTATCCTTCTCGCTGTAACAATCATCTATCAGTACTTTGAAATCTTTGTGAAGGAA
CAAAGTGAAGGTTTAGGAATGGGCAGTTTACTGTTTTAA

>g14212.t11 Gene=g14212 Length=472
MGIKFLEVIKPFCSILPEVTKPERKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGVKIIEVGDTPKDRALFNGAQKLFG
MVITIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRGLREAFYRQNLP
NLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSN
LYMLAVKFHGNFLVNLLGVWADVGGGGPARSYPIGGLCYYFSPPESLGHILQDPVHAVLY
IIFMLGSCAFFSKTWIDVSGSSAKDVAKQLKEQQMVMRGHRENSMIHELNRYIPTAAAFG
GLCIGALSVMADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEGLGMGSLLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g14212.t11 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 28 469 2.4E-181
3 g14212.t11 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 1 471 0.0
4 g14212.t11 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 1 471 0.0
28 g14212.t11 PIRSF PIRSF004557 SecY_Sec61alpha 6 464 3.2E-96
1 g14212.t11 Pfam PF10559 Plug domain of Sec61p 40 74 8.1E-17
2 g14212.t11 Pfam PF00344 SecY translocase 75 453 4.3E-77
9 g14212.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 31 -
18 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 54 -
15 g14212.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 55 73 -
22 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 97 -
12 g14212.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 98 117 -
27 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 137 -
14 g14212.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 138 142 -
26 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
8 g14212.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 166 171 -
21 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 172 193 -
13 g14212.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 194 241 -
25 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 242 263 -
11 g14212.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 264 282 -
20 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 283 305 -
17 g14212.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 306 356 -
19 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 357 376 -
10 g14212.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 377 408 -
24 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 409 427 -
16 g14212.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 428 432 -
23 g14212.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 433 454 -
7 g14212.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 455 472 -
40 g14212.t11 ProSitePatterns PS00755 Protein secY signature 1. 75 94 -
39 g14212.t11 ProSitePatterns PS00756 Protein secY signature 2. 164 182 -
5 g14212.t11 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 8 460 1.57E-121
41 g14212.t11 TIGRFAM TIGR00967 3a0501s007: preprotein translocase, SecY subunit 29 461 5.1E-119
31 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -
32 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 75 97 -
30 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 138 -
38 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
36 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 241 263 -
29 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 283 305 -
34 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 312 334 -
33 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 354 376 -
35 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 409 431 -
37 g14212.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 436 458 -

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