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.t9 TTS g14212.t9 35445352 35445352
chr_1 g14212 g14212.t9 isoform g14212.t9 35445873 35447733
chr_1 g14212 g14212.t9 exon g14212.t9.exon1 35445873 35446385
chr_1 g14212 g14212.t9 cds g14212.t9.CDS1 35445873 35446385
chr_1 g14212 g14212.t9 exon g14212.t9.exon2 35446458 35446861
chr_1 g14212 g14212.t9 cds g14212.t9.CDS2 35446458 35446861
chr_1 g14212 g14212.t9 exon g14212.t9.exon3 35446944 35447382
chr_1 g14212 g14212.t9 cds g14212.t9.CDS3 35446944 35447382
chr_1 g14212 g14212.t9 exon g14212.t9.exon4 35447494 35447552
chr_1 g14212 g14212.t9 cds g14212.t9.CDS4 35447494 35447552
chr_1 g14212 g14212.t9 exon g14212.t9.exon5 35447727 35447733
chr_1 g14212 g14212.t9 cds g14212.t9.CDS5 35447727 35447733
chr_1 g14212 g14212.t9 TSS g14212.t9 35447866 35447866

Sequences

>g14212.t9 Gene=g14212 Length=1422
ATGGGAATGGAAGTTATAAAACCATTTTGCAGCATTCTGCCGGAAGTAACGAAGCCAGAA
CGAAAGATCCAATTTCGTGAAAAAGTGCTATGGACCGCAATAACTTTATTCATTTTCCTG
GTATGTTGTCAAATTCCACTATTCGGTATAATGTCATCAGATTCAGCCGATCCTTTCTAT
TGGATTCGTGTTATTCTCGCTTCTAATCGTGGTACTTTAATGGAATTGGGTATTTCCCCA
ATTGTCACATCTGGTCTCATTATGCAATTACTTGCTGGTGTTAAAATTATTGAAGTCGGT
GATACACCAAAAGACAGGGCACTTTTTAACGGCGCACAGAAACTCTTTGGCATGGTCATC
ACAATTGGTCAGGCAATTGTATACGTAATGACAGGAATGTATGGTGATCCAGCAGAAATT
GGTGCCGGTGTCTGTCTACTCATCATCATTCAACTCTTTGTTGCTGGTCTTATCGTTCTT
TTGCTCGATGAGTTACTTCAAAAAGGTTACGGTTTGGGTTCTGGAATTTCACTTTTCATT
GCAACGAACATTTGTGAGACAATCGTATGGAAAGCATTTTCACCTGCAACTGTTAACACT
GGTCGTGGTACAGAATTCGAGGGCGCTGTAATTGCACTGTTCCATCTTCTTGCAACACGT
CAAGACAAAGTTCGTGGTTTACGAGAGGCTTTTTATCGTCAAAATTTGCCCAATTTAATG
AACTTGCTTGCTACCGTACTCGTCTTTGCTATAGTTATATACTTCCAAGGATTCCGTGTC
GATTTGCCAATCAAATCAGCTCGCTATCGCGGTCAATACAGCAGTTATCCAATCAAACTT
TTCTATACATCAAACATTCCCATCATCTTGCAATCGGCACTTGTTTCAAATCTTTACGTT
ATTTCACAGATGCTTGCTGTTAAATTTCATGGAAACTTCCTTGTAAACCTATTAGGAGTT
TGGGCTGATGTCGGTGGTGGCGGTCCAGCAAGATCATACCCTATTGGAGGTTTATGCTAC
TATTTTTCACCACCAGAAAGTCTTGGTCACATCTTGCAAGATCCAGTTCATGCAGTTCTC
TATATTATTTTTATGCTCGGTTCATGCGCTTTCTTCTCAAAAACGTGGATTGATGTTTCA
GGAAGCTCTGCCAAGGATGTTGCAAAACAATTGAAAGAACAACAAATGGTTATGCGTGGA
CATCGTGAAAACTCAATGATTCATGAGTTGAATCGTTACATCCCAACTGCAGCTGCTTTC
GGTGGTCTCTGCATTGGTGCACTCTCAGTAATGGCTGATTTCCTCGGAGCTATTGGTTCA
GGAACTGGTATCCTTCTCGCTGTAACAATCATCTATCAGTACTTTGAAATCTTTGTGAAG
GAACAAAGTGAAGGTTTAGGAATGGGCAGTTTACTGTTTTAA

>g14212.t9 Gene=g14212 Length=473
MGMEVIKPFCSILPEVTKPERKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSADPFY
WIRVILASNRGTLMELGISPIVTSGLIMQLLAGVKIIEVGDTPKDRALFNGAQKLFGMVI
TIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKGYGLGSGISLFI
ATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRGLREAFYRQNLPNLM
NLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLYV
ISQMLAVKFHGNFLVNLLGVWADVGGGGPARSYPIGGLCYYFSPPESLGHILQDPVHAVL
YIIFMLGSCAFFSKTWIDVSGSSAKDVAKQLKEQQMVMRGHRENSMIHELNRYIPTAAAF
GGLCIGALSVMADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEGLGMGSLLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g14212.t9 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 25 470 1.3E-182
3 g14212.t9 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 3 472 0.0
4 g14212.t9 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 3 472 0.0
28 g14212.t9 PIRSF PIRSF004557 SecY_Sec61alpha 3 465 5.3E-97
1 g14212.t9 Pfam PF10559 Plug domain of Sec61p 37 71 8.1E-17
2 g14212.t9 Pfam PF00344 SecY translocase 72 454 4.0E-77
12 g14212.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 28 -
23 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 29 51 -
13 g14212.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 52 70 -
24 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 71 94 -
9 g14212.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 95 114 -
26 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 134 -
16 g14212.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 139 -
27 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 162 -
11 g14212.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 163 168 -
19 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 169 190 -
15 g14212.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 191 238 -
22 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 239 260 -
7 g14212.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 261 279 -
18 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 280 301 -
14 g14212.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 302 357 -
21 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 358 377 -
8 g14212.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 378 409 -
20 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 410 428 -
17 g14212.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 429 433 -
25 g14212.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 434 455 -
10 g14212.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 456 473 -
40 g14212.t9 ProSitePatterns PS00755 Protein secY signature 1. 72 91 -
39 g14212.t9 ProSitePatterns PS00756 Protein secY signature 2. 161 179 -
5 g14212.t9 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 5 461 5.75E-124
41 g14212.t9 TIGRFAM TIGR00967 3a0501s007: preprotein translocase, SecY subunit 26 462 9.0E-121
33 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 30 52 -
29 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 72 94 -
32 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 135 -
38 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 140 162 -
31 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 236 258 -
36 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 278 300 -
34 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 313 335 -
37 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 355 377 -
30 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 410 432 -
35 g14212.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 437 459 -

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