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.t8 TTS g14212.t8 35445352 35445352
chr_1 g14212 g14212.t8 isoform g14212.t8 35445873 35447733
chr_1 g14212 g14212.t8 exon g14212.t8.exon1 35445873 35446385
chr_1 g14212 g14212.t8 cds g14212.t8.CDS1 35445873 35446385
chr_1 g14212 g14212.t8 exon g14212.t8.exon2 35446458 35446861
chr_1 g14212 g14212.t8 cds g14212.t8.CDS2 35446458 35446861
chr_1 g14212 g14212.t8 exon g14212.t8.exon3 35446944 35447153
chr_1 g14212 g14212.t8 cds g14212.t8.CDS3 35446944 35447153
chr_1 g14212 g14212.t8 exon g14212.t8.exon4 35447329 35447382
chr_1 g14212 g14212.t8 cds g14212.t8.CDS4 35447329 35447359
chr_1 g14212 g14212.t8 exon g14212.t8.exon5 35447494 35447561
chr_1 g14212 g14212.t8 exon g14212.t8.exon6 35447727 35447733
chr_1 g14212 g14212.t8 TSS g14212.t8 35447866 35447866

Sequences

>g14212.t8 Gene=g14212 Length=1256
ATGGGAATTAAATTCCTGGAAGTTATAAAACCATTTTGCAGCATTCTGCCGGAAGTAACG
AAGCCAGAACGAAAGATCCAATTTCGTGAAAAAGTGCTATGGACCGCAATAACTTTATTC
ATTTTCCTGTCGGTGATACACCAAAAGACAGGGCACTTTTTAACGGCGCACAGAAACTCT
TTGGCATGGTCATCACAATTGGTCAGGCAATTGTATACGTAATGACAGGAATGTATGGTG
ATCCAGCAGAAATTGGTGCCGGTGTCTGTCTACTCATCATCATTCAACTCTTTGTTGCTG
GTCTTATCGTTCTTTTGCTCGATGAGTTACTTCAAAAAGGTTACGGTTTGGGTTCTGGAA
TTTCACTTTTCATTGCAACGAACATTTGTGAGACAATCGTATGGAAAGCATTTTCACCTG
CAACTGTTAACACTGGTCGTGGTACAGAATTCGAGGGCGCTGTAATTGCACTGTTCCATC
TTCTTGCAACACGTCAAGACAAAGTTCGTGGTTTACGAGAGGCTTTTTATCGTCAAAATT
TGCCCAATTTAATGAACTTGCTTGCTACCGTACTCGTCTTTGCTATAGTTATATACTTCC
AAGGATTCCGTGTCGATTTGCCAATCAAATCAGCTCGCTATCGCGGTCAATACAGCAGTT
ATCCAATCAAACTTTTCTATACATCAAACATTCCCATCATCTTGCAATCGGCACTTGTTT
CAAATCTTTACGTTATTTCACAGATGCTTGCTGTTAAATTTCATGGAAACTTCCTTGTAA
ACCTATTAGGAGTTTGGGCTGATGTCGGTGGTGGCGGTCCAGCAAGATCATACCCTATTG
GAGGTTTATGCTACTATTTTTCACCACCAGAAAGTCTTGGTCACATCTTGCAAGATCCAG
TTCATGCAGTTCTCTATATTATTTTTATGCTCGGTTCATGCGCTTTCTTCTCAAAAACGT
GGATTGATGTTTCAGGAAGCTCTGCCAAGGATGTTGCAAAACAATTGAAAGAACAACAAA
TGGTTATGCGTGGACATCGTGAAAACTCAATGATTCATGAGTTGAATCGTTACATCCCAA
CTGCAGCTGCTTTCGGTGGTCTCTGCATTGGTGCACTCTCAGTAATGGCTGATTTCCTCG
GAGCTATTGGTTCAGGAACTGGTATCCTTCTCGCTGTAACAATCATCTATCAGTACTTTG
AAATCTTTGTGAAGGAACAAAGTGAAGGTTTAGGAATGGGCAGTTTACTGTTTTAA

>g14212.t8 Gene=g14212 Length=385
MDRNNFIHFPVGDTPKDRALFNGAQKLFGMVITIGQAIVYVMTGMYGDPAEIGAGVCLLI
IIQLFVAGLIVLLLDELLQKGYGLGSGISLFIATNICETIVWKAFSPATVNTGRGTEFEG
AVIALFHLLATRQDKVRGLREAFYRQNLPNLMNLLATVLVFAIVIYFQGFRVDLPIKSAR
YRGQYSSYPIKLFYTSNIPIILQSALVSNLYVISQMLAVKFHGNFLVNLLGVWADVGGGG
PARSYPIGGLCYYFSPPESLGHILQDPVHAVLYIIFMLGSCAFFSKTWIDVSGSSAKDVA
KQLKEQQMVMRGHRENSMIHELNRYIPTAAAFGGLCIGALSVMADFLGAIGSGTGILLAV
TIIYQYFEIFVKEQSEGLGMGSLLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g14212.t8 Gene3D G3DSA:1.10.3370.10 Preprotein translocase SecY subunit domain 10 382 3.3E-147
2 g14212.t8 PANTHER PTHR10906 SECY/SEC61-ALPHA FAMILY MEMBER 11 384 6.2E-241
3 g14212.t8 PANTHER PTHR10906:SF10 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 11 384 6.2E-241
23 g14212.t8 PIRSF PIRSF004557 SecY_Sec61alpha 12 377 1.2E-68
1 g14212.t8 Pfam PF00344 SecY translocase 14 366 1.7E-67
7 g14212.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 26 -
18 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 27 46 -
13 g14212.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 47 51 -
16 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 74 -
10 g14212.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 75 80 -
17 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 81 102 -
14 g14212.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 103 150 -
22 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 151 172 -
9 g14212.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 173 191 -
21 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 192 213 -
12 g14212.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 214 269 -
19 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 270 289 -
6 g14212.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 290 321 -
15 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 322 340 -
11 g14212.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 341 345 -
20 g14212.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 346 367 -
8 g14212.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 368 385 -
32 g14212.t8 ProSitePatterns PS00756 Protein secY signature 2. 73 91 -
4 g14212.t8 SUPERFAMILY SSF103491 Preprotein translocase SecY subunit 14 373 3.53E-92
33 g14212.t8 TIGRFAM TIGR00967 3a0501s007: preprotein translocase, SecY subunit 13 374 1.2E-95
28 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
27 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 74 -
31 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 148 170 -
26 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 190 212 -
29 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 225 247 -
24 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 267 289 -
30 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 322 344 -
25 g14212.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 349 371 -

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