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.t7 TTS g14212.t7 35445352 35445352
chr_1 g14212 g14212.t7 isoform g14212.t7 35445873 35447733
chr_1 g14212 g14212.t7 exon g14212.t7.exon1 35445873 35446385
chr_1 g14212 g14212.t7 cds g14212.t7.CDS1 35445873 35446385
chr_1 g14212 g14212.t7 exon g14212.t7.exon2 35446458 35446861
chr_1 g14212 g14212.t7 cds g14212.t7.CDS2 35446458 35446861
chr_1 g14212 g14212.t7 exon g14212.t7.exon3 35446944 35447033
chr_1 g14212 g14212.t7 cds g14212.t7.CDS3 35446944 35447033
chr_1 g14212 g14212.t7 exon g14212.t7.exon4 35447106 35447382
chr_1 g14212 g14212.t7 cds g14212.t7.CDS4 35447106 35447298
chr_1 g14212 g14212.t7 exon g14212.t7.exon5 35447494 35447733
chr_1 g14212 g14212.t7 TSS g14212.t7 35447866 35447866

Sequences

>g14212.t7 Gene=g14212 Length=1524
ATGGGAAGTAAGTGAATTGAATTTCATTCAAAATTAGTGCGAAATGTGGATTTCCATGAA
AAATTTATGCTGCATTCAATTAAGAAATGTTGCTTTGTTGGCAATCTTTAAGATCTAATT
TGCACTAAATCTCTTTATTTCTAATGTACTTTACGTGATTTTTCTTATCTAGTTAAATTC
CTGGAAGTTATAAAACCATTTTGCAGCATTCTGCCGGAAGTAACGAAGCCAGAACGAAAG
ATCCAATTTCGTGAAAAAGTGCTATGGACCGCAATAACTTTATTCATTTTCCTGGTATGT
TGTCAAATTCCACTATTCGGTATAATGTCATCAGATTCAGCCGATCCTTTCTATTGGATT
CGTGTTATTCTCGCTTCTAATCGTGGTACTTTAATGGAATTGGGTATTTCCCCAATTGTC
ACATCTGGTCTCATTATGCAATTACTTGCTGGTGTTAAAATTATTGAAGTCGGTGATACA
CCAAAAGACAGGGCACTTTTTAACGGCGCACAGAAACAAATTGGTGCCGGTGTCTGTCTA
CTCATCATCATTCAACTCTTTGTTGCTGGTCTTATCGTTCTTTTGCTCGATGAGTTACTT
CAAAAAGGTTACGGTTTGGGTTCTGGAATTTCACTTTTCATTGCAACGAACATTTGTGAG
ACAATCGTATGGAAAGCATTTTCACCTGCAACTGTTAACACTGGTCGTGGTACAGAATTC
GAGGGCGCTGTAATTGCACTGTTCCATCTTCTTGCAACACGTCAAGACAAAGTTCGTGGT
TTACGAGAGGCTTTTTATCGTCAAAATTTGCCCAATTTAATGAACTTGCTTGCTACCGTA
CTCGTCTTTGCTATAGTTATATACTTCCAAGGATTCCGTGTCGATTTGCCAATCAAATCA
GCTCGCTATCGCGGTCAATACAGCAGTTATCCAATCAAACTTTTCTATACATCAAACATT
CCCATCATCTTGCAATCGGCACTTGTTTCAAATCTTTACGTTATTTCACAGATGCTTGCT
GTTAAATTTCATGGAAACTTCCTTGTAAACCTATTAGGAGTTTGGGCTGATGTCGGTGGT
GGCGGTCCAGCAAGATCATACCCTATTGGAGGTTTATGCTACTATTTTTCACCACCAGAA
AGTCTTGGTCACATCTTGCAAGATCCAGTTCATGCAGTTCTCTATATTATTTTTATGCTC
GGTTCATGCGCTTTCTTCTCAAAAACGTGGATTGATGTTTCAGGAAGCTCTGCCAAGGAT
GTTGCAAAACAATTGAAAGAACAACAAATGGTTATGCGTGGACATCGTGAAAACTCAATG
ATTCATGAGTTGAATCGTTACATCCCAACTGCAGCTGCTTTCGGTGGTCTCTGCATTGGT
GCACTCTCAGTAATGGCTGATTTCCTCGGAGCTATTGGTTCAGGAACTGGTATCCTTCTC
GCTGTAACAATCATCTATCAGTACTTTGAAATCTTTGTGAAGGAACAAAGTGAAGGTTTA
GGAATGGGCAGTTTACTGTTTTAA

>g14212.t7 Gene=g14212 Length=399
MSSDSADPFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGVKIIEVGDTPKDRALFN
GAQKQIGAGVCLLIIIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFS
PATVNTGRGTEFEGAVIALFHLLATRQDKVRGLREAFYRQNLPNLMNLLATVLVFAIVIY
FQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSNLYVISQMLAVKFHGNFL
VNLLGVWADVGGGGPARSYPIGGLCYYFSPPESLGHILQDPVHAVLYIIFMLGSCAFFSK
TWIDVSGSSAKDVAKQLKEQQMVMRGHRENSMIHELNRYIPTAAAFGGLCIGALSVMADF
LGAIGSGTGILLAVTIIYQYFEIFVKEQSEGLGMGSLLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g14212.t7 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 1 395 2.9E-154
3 g14212.t7 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 1 67 1.6E-248
5 g14212.t7 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 1 67 1.6E-248
4 g14212.t7 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 65 398 1.6E-248
6 g14212.t7 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 65 398 1.6E-248
28 g14212.t7 PIRSF PIRSF004557 SecY_Sec61alpha 2 71 1.9E-10
27 g14212.t7 PIRSF PIRSF004557 SecY_Sec61alpha 59 391 3.9E-63
9 g14212.t7 PRINTS PR00303 Preprotein translocase SecY subunit signature 21 41 1.1E-5
8 g14212.t7 PRINTS PR00303 Preprotein translocase SecY subunit signature 281 303 1.1E-5
7 g14212.t7 PRINTS PR00303 Preprotein translocase SecY subunit signature 366 384 1.1E-5
1 g14212.t7 Pfam PF10559 Plug domain of Sec61p 2 21 1.9E-6
2 g14212.t7 Pfam PF00344 SecY translocase 22 380 1.3E-67
19 g14212.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
21 g14212.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 47 -
15 g14212.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 67 -
20 g14212.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 88 -
16 g14212.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 89 164 -
26 g14212.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 165 186 -
13 g14212.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 187 205 -
25 g14212.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 206 227 -
18 g14212.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 228 283 -
24 g14212.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 284 303 -
14 g14212.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 304 335 -
22 g14212.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 336 354 -
17 g14212.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 355 359 -
23 g14212.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 360 381 -
12 g14212.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 382 399 -
38 g14212.t7 ProSitePatterns PS00755 Protein secY signature 1. 22 41 -
37 g14212.t7 ProSitePatterns PS00756 Protein secY signature 2. 87 105 -
10 g14212.t7 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 3 387 6.93E-102
39 g14212.t7 TIGRFAM TIGR00967 3a0501s007: preprotein translocase, SecY subunit 66 388 3.9E-84
34 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
36 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 120 -
33 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 162 184 -
31 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 204 226 -
30 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 239 261 -
35 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 281 303 -
29 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 336 358 -
32 g14212.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 363 385 -

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. There were no conditions that were differentially expressed