General information for g14212.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein transport protein Sec61 subunit alpha isoform 2.
Parent gene
- The parent gene g14212 is located on chr_1: 35446942..35447864 (- strand)
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.t1 | TTS | g14212.t1 | 35445352 | 35445352 |
| chr_1 | g14212 | g14212.t1 | isoform | g14212.t1 | 35445873 | 35447733 |
| chr_1 | g14212 | g14212.t1 | exon | g14212.t1.exon1 | 35445873 | 35446385 |
| chr_1 | g14212 | g14212.t1 | cds | g14212.t1.CDS1 | 35445873 | 35446385 |
| chr_1 | g14212 | g14212.t1 | exon | g14212.t1.exon2 | 35446458 | 35446861 |
| chr_1 | g14212 | g14212.t1 | cds | g14212.t1.CDS2 | 35446458 | 35446861 |
| chr_1 | g14212 | g14212.t1 | exon | g14212.t1.exon3 | 35446944 | 35447382 |
| chr_1 | g14212 | g14212.t1 | cds | g14212.t1.CDS3 | 35446944 | 35447382 |
| chr_1 | g14212 | g14212.t1 | exon | g14212.t1.exon4 | 35447494 | 35447561 |
| chr_1 | g14212 | g14212.t1 | cds | g14212.t1.CDS4 | 35447494 | 35447561 |
| chr_1 | g14212 | g14212.t1 | exon | g14212.t1.exon5 | 35447727 | 35447733 |
| chr_1 | g14212 | g14212.t1 | cds | g14212.t1.CDS5 | 35447727 | 35447733 |
| chr_1 | g14212 | g14212.t1 | TSS | g14212.t1 | 35447866 | 35447866 |
Sequences
>g14212.t1 Gene=g14212 Length=1431
ATGGGAATTAAATTCCTGGAAGTTATAAAACCATTTTGCAGCATTCTGCCGGAAGTAACG
AAGCCAGAACGAAAGATCCAATTTCGTGAAAAAGTGCTATGGACCGCAATAACTTTATTC
ATTTTCCTGGTATGTTGTCAAATTCCACTATTCGGTATAATGTCATCAGATTCAGCCGAT
CCTTTCTATTGGATTCGTGTTATTCTCGCTTCTAATCGTGGTACTTTAATGGAATTGGGT
ATTTCCCCAATTGTCACATCTGGTCTCATTATGCAATTACTTGCTGGTGTTAAAATTATT
GAAGTCGGTGATACACCAAAAGACAGGGCACTTTTTAACGGCGCACAGAAACTCTTTGGC
ATGGTCATCACAATTGGTCAGGCAATTGTATACGTAATGACAGGAATGTATGGTGATCCA
GCAGAAATTGGTGCCGGTGTCTGTCTACTCATCATCATTCAACTCTTTGTTGCTGGTCTT
ATCGTTCTTTTGCTCGATGAGTTACTTCAAAAAGGTTACGGTTTGGGTTCTGGAATTTCA
CTTTTCATTGCAACGAACATTTGTGAGACAATCGTATGGAAAGCATTTTCACCTGCAACT
GTTAACACTGGTCGTGGTACAGAATTCGAGGGCGCTGTAATTGCACTGTTCCATCTTCTT
GCAACACGTCAAGACAAAGTTCGTGGTTTACGAGAGGCTTTTTATCGTCAAAATTTGCCC
AATTTAATGAACTTGCTTGCTACCGTACTCGTCTTTGCTATAGTTATATACTTCCAAGGA
TTCCGTGTCGATTTGCCAATCAAATCAGCTCGCTATCGCGGTCAATACAGCAGTTATCCA
ATCAAACTTTTCTATACATCAAACATTCCCATCATCTTGCAATCGGCACTTGTTTCAAAT
CTTTACGTTATTTCACAGATGCTTGCTGTTAAATTTCATGGAAACTTCCTTGTAAACCTA
TTAGGAGTTTGGGCTGATGTCGGTGGTGGCGGTCCAGCAAGATCATACCCTATTGGAGGT
TTATGCTACTATTTTTCACCACCAGAAAGTCTTGGTCACATCTTGCAAGATCCAGTTCAT
GCAGTTCTCTATATTATTTTTATGCTCGGTTCATGCGCTTTCTTCTCAAAAACGTGGATT
GATGTTTCAGGAAGCTCTGCCAAGGATGTTGCAAAACAATTGAAAGAACAACAAATGGTT
ATGCGTGGACATCGTGAAAACTCAATGATTCATGAGTTGAATCGTTACATCCCAACTGCA
GCTGCTTTCGGTGGTCTCTGCATTGGTGCACTCTCAGTAATGGCTGATTTCCTCGGAGCT
ATTGGTTCAGGAACTGGTATCCTTCTCGCTGTAACAATCATCTATCAGTACTTTGAAATC
TTTGTGAAGGAACAAAGTGAAGGTTTAGGAATGGGCAGTTTACTGTTTTAA
>g14212.t1 Gene=g14212 Length=476
MGIKFLEVIKPFCSILPEVTKPERKIQFREKVLWTAITLFIFLVCCQIPLFGIMSSDSAD
PFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGVKIIEVGDTPKDRALFNGAQKLFG
MVITIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKGYGLGSGIS
LFIATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRGLREAFYRQNLP
NLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIILQSALVSN
LYVISQMLAVKFHGNFLVNLLGVWADVGGGGPARSYPIGGLCYYFSPPESLGHILQDPVH
AVLYIIFMLGSCAFFSKTWIDVSGSSAKDVAKQLKEQQMVMRGHRENSMIHELNRYIPTA
AAFGGLCIGALSVMADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEGLGMGSLLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g14212.t1 | Gene3D | G3DSA:1.10.3370.10 | Preprotein translocase SecY subunit domain | 28 | 473 | 1.4E-182 |
| 3 | g14212.t1 | PANTHER | PTHR10906 | SECY/SEC61-ALPHA FAMILY MEMBER | 1 | 475 | 0.0 |
| 4 | g14212.t1 | PANTHER | PTHR10906:SF10 | PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 | 1 | 475 | 0.0 |
| 28 | g14212.t1 | PIRSF | PIRSF004557 | SecY_Sec61alpha | 6 | 468 | 6.8E-97 |
| 1 | g14212.t1 | Pfam | PF10559 | Plug domain of Sec61p | 40 | 74 | 8.2E-17 |
| 2 | g14212.t1 | Pfam | PF00344 | SecY translocase | 75 | 457 | 4.1E-77 |
| 8 | g14212.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 31 | - |
| 18 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 54 | - |
| 16 | g14212.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 55 | 73 | - |
| 22 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 97 | - |
| 11 | g14212.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 98 | 117 | - |
| 27 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 118 | 137 | - |
| 14 | g14212.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 138 | 142 | - |
| 25 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 165 | - |
| 7 | g14212.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 166 | 171 | - |
| 20 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 172 | 193 | - |
| 13 | g14212.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 194 | 241 | - |
| 24 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 242 | 263 | - |
| 10 | g14212.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 264 | 282 | - |
| 21 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 304 | - |
| 17 | g14212.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 305 | 360 | - |
| 23 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 361 | 380 | - |
| 12 | g14212.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 381 | 412 | - |
| 26 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 413 | 431 | - |
| 15 | g14212.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 432 | 436 | - |
| 19 | g14212.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 437 | 458 | - |
| 9 | g14212.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 459 | 476 | - |
| 40 | g14212.t1 | ProSitePatterns | PS00755 | Protein secY signature 1. | 75 | 94 | - |
| 39 | g14212.t1 | ProSitePatterns | PS00756 | Protein secY signature 2. | 164 | 182 | - |
| 5 | g14212.t1 | SUPERFAMILY | SSF103491 | Preprotein translocase SecY subunit | 8 | 464 | 5.89E-124 |
| 41 | g14212.t1 | TIGRFAM | TIGR00967 | 3a0501s007: preprotein translocase, SecY subunit | 29 | 465 | 9.2E-121 |
| 34 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 33 | 55 | - |
| 35 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 75 | 97 | - |
| 30 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 118 | 138 | - |
| 38 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 165 | - |
| 31 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 239 | 261 | - |
| 36 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 281 | 303 | - |
| 33 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 316 | 338 | - |
| 37 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 358 | 380 | - |
| 29 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 413 | 435 | - |
| 32 | g14212.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 440 | 462 | - |
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 transcript has been annotated with K10956 (protein transport protein SEC61 subunit alpha)
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.
