General information for g14212.t10
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.t10 | TTS | g14212.t10 | 35445352 | 35445352 |
| chr_1 | g14212 | g14212.t10 | isoform | g14212.t10 | 35445873 | 35447733 |
| chr_1 | g14212 | g14212.t10 | exon | g14212.t10.exon1 | 35445873 | 35446385 |
| chr_1 | g14212 | g14212.t10 | cds | g14212.t10.CDS1 | 35445873 | 35446385 |
| chr_1 | g14212 | g14212.t10 | exon | g14212.t10.exon2 | 35446458 | 35446861 |
| chr_1 | g14212 | g14212.t10 | cds | g14212.t10.CDS2 | 35446458 | 35446861 |
| chr_1 | g14212 | g14212.t10 | exon | g14212.t10.exon3 | 35446944 | 35447382 |
| chr_1 | g14212 | g14212.t10 | cds | g14212.t10.CDS3 | 35446944 | 35447298 |
| chr_1 | g14212 | g14212.t10 | exon | g14212.t10.exon4 | 35447689 | 35447733 |
| chr_1 | g14212 | g14212.t10 | TSS | g14212.t10 | 35447866 | 35447866 |
Sequences
>g14212.t10 Gene=g14212 Length=1401
ATGGGAAGTAAGTGAATTGAATTTCATTCAAAATTAGTGCGAAATATCCAATTTCGTGAA
AAAGTGCTATGGACCGCAATAACTTTATTCATTTTCCTGGTATGTTGTCAAATTCCACTA
TTCGGTATAATGTCATCAGATTCAGCCGATCCTTTCTATTGGATTCGTGTTATTCTCGCT
TCTAATCGTGGTACTTTAATGGAATTGGGTATTTCCCCAATTGTCACATCTGGTCTCATT
ATGCAATTACTTGCTGGTGTTAAAATTATTGAAGTCGGTGATACACCAAAAGACAGGGCA
CTTTTTAACGGCGCACAGAAACTCTTTGGCATGGTCATCACAATTGGTCAGGCAATTGTA
TACGTAATGACAGGAATGTATGGTGATCCAGCAGAAATTGGTGCCGGTGTCTGTCTACTC
ATCATCATTCAACTCTTTGTTGCTGGTCTTATCGTTCTTTTGCTCGATGAGTTACTTCAA
AAAGGTTACGGTTTGGGTTCTGGAATTTCACTTTTCATTGCAACGAACATTTGTGAGACA
ATCGTATGGAAAGCATTTTCACCTGCAACTGTTAACACTGGTCGTGGTACAGAATTCGAG
GGCGCTGTAATTGCACTGTTCCATCTTCTTGCAACACGTCAAGACAAAGTTCGTGGTTTA
CGAGAGGCTTTTTATCGTCAAAATTTGCCCAATTTAATGAACTTGCTTGCTACCGTACTC
GTCTTTGCTATAGTTATATACTTCCAAGGATTCCGTGTCGATTTGCCAATCAAATCAGCT
CGCTATCGCGGTCAATACAGCAGTTATCCAATCAAACTTTTCTATACATCAAACATTCCC
ATCATCTTGCAATCGGCACTTGTTTCAAATCTTTACGTTATTTCACAGATGCTTGCTGTT
AAATTTCATGGAAACTTCCTTGTAAACCTATTAGGAGTTTGGGCTGATGTCGGTGGTGGC
GGTCCAGCAAGATCATACCCTATTGGAGGTTTATGCTACTATTTTTCACCACCAGAAAGT
CTTGGTCACATCTTGCAAGATCCAGTTCATGCAGTTCTCTATATTATTTTTATGCTCGGT
TCATGCGCTTTCTTCTCAAAAACGTGGATTGATGTTTCAGGAAGCTCTGCCAAGGATGTT
GCAAAACAATTGAAAGAACAACAAATGGTTATGCGTGGACATCGTGAAAACTCAATGATT
CATGAGTTGAATCGTTACATCCCAACTGCAGCTGCTTTCGGTGGTCTCTGCATTGGTGCA
CTCTCAGTAATGGCTGATTTCCTCGGAGCTATTGGTTCAGGAACTGGTATCCTTCTCGCT
GTAACAATCATCTATCAGTACTTTGAAATCTTTGTGAAGGAACAAAGTGAAGGTTTAGGA
ATGGGCAGTTTACTGTTTTAA
>g14212.t10 Gene=g14212 Length=423
MSSDSADPFYWIRVILASNRGTLMELGISPIVTSGLIMQLLAGVKIIEVGDTPKDRALFN
GAQKLFGMVITIGQAIVYVMTGMYGDPAEIGAGVCLLIIIQLFVAGLIVLLLDELLQKGY
GLGSGISLFIATNICETIVWKAFSPATVNTGRGTEFEGAVIALFHLLATRQDKVRGLREA
FYRQNLPNLMNLLATVLVFAIVIYFQGFRVDLPIKSARYRGQYSSYPIKLFYTSNIPIIL
QSALVSNLYVISQMLAVKFHGNFLVNLLGVWADVGGGGPARSYPIGGLCYYFSPPESLGH
ILQDPVHAVLYIIFMLGSCAFFSKTWIDVSGSSAKDVAKQLKEQQMVMRGHRENSMIHEL
NRYIPTAAAFGGLCIGALSVMADFLGAIGSGTGILLAVTIIYQYFEIFVKEQSEGLGMGS
LLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g14212.t10 | Gene3D | G3DSA:1.10.3370.10 | Preprotein translocase SecY subunit domain | 1 | 420 | 4.3E-170 |
| 3 | g14212.t10 | PANTHER | PTHR10906 | SECY/SEC61-ALPHA FAMILY MEMBER | 1 | 422 | 9.0E-274 |
| 4 | g14212.t10 | PANTHER | PTHR10906:SF10 | PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 2 | 1 | 422 | 9.0E-274 |
| 29 | g14212.t10 | PIRSF | PIRSF004557 | SecY_Sec61alpha | 2 | 415 | 1.7E-81 |
| 6 | g14212.t10 | PRINTS | PR00303 | Preprotein translocase SecY subunit signature | 21 | 41 | 1.2E-5 |
| 7 | g14212.t10 | PRINTS | PR00303 | Preprotein translocase SecY subunit signature | 305 | 327 | 1.2E-5 |
| 5 | g14212.t10 | PRINTS | PR00303 | Preprotein translocase SecY subunit signature | 390 | 408 | 1.2E-5 |
| 1 | g14212.t10 | Pfam | PF10559 | Plug domain of Sec61p | 2 | 21 | 2.0E-6 |
| 2 | g14212.t10 | Pfam | PF00344 | SecY translocase | 22 | 404 | 2.7E-77 |
| 19 | g14212.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 25 | - |
| 22 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 44 | - |
| 12 | g14212.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 45 | 64 | - |
| 28 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 65 | 84 | - |
| 18 | g14212.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 85 | 89 | - |
| 21 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 90 | 112 | - |
| 11 | g14212.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 113 | 118 | - |
| 27 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 119 | 140 | - |
| 17 | g14212.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 141 | 188 | - |
| 20 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 189 | 210 | - |
| 10 | g14212.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 211 | 229 | - |
| 24 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 230 | 251 | - |
| 16 | g14212.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 252 | 307 | - |
| 23 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 308 | 327 | - |
| 13 | g14212.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 328 | 359 | - |
| 25 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 360 | 378 | - |
| 15 | g14212.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 379 | 383 | - |
| 26 | g14212.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 405 | - |
| 14 | g14212.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 406 | 423 | - |
| 40 | g14212.t10 | ProSitePatterns | PS00755 | Protein secY signature 1. | 22 | 41 | - |
| 39 | g14212.t10 | ProSitePatterns | PS00756 | Protein secY signature 2. | 111 | 129 | - |
| 8 | g14212.t10 | SUPERFAMILY | SSF103491 | Preprotein translocase SecY subunit | 3 | 411 | 2.35E-109 |
| 41 | g14212.t10 | TIGRFAM | TIGR00967 | 3a0501s007: preprotein translocase, SecY subunit | 4 | 412 | 8.2E-111 |
| 38 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 22 | 44 | - |
| 34 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 65 | 85 | - |
| 30 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 90 | 112 | - |
| 37 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 208 | - |
| 36 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 228 | 250 | - |
| 33 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 263 | 285 | - |
| 35 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 305 | 327 | - |
| 32 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 360 | 382 | - |
| 31 | g14212.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 387 | 409 | - |
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. There were no conditions that were differentially expressed