General information for g10780.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g10780 is located on chr_1: 11912374..11914241 (+ 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 | g10780 | g10780.t1 | isoform | g10780.t1 | 11912374 | 11914241 |
| chr_1 | g10780 | g10780.t1 | exon | g10780.t1.exon1 | 11912374 | 11913077 |
| chr_1 | g10780 | g10780.t1 | cds | g10780.t1.CDS1 | 11912374 | 11913077 |
| chr_1 | g10780 | g10780.t1 | exon | g10780.t1.exon2 | 11913130 | 11913723 |
| chr_1 | g10780 | g10780.t1 | cds | g10780.t1.CDS2 | 11913130 | 11913723 |
| chr_1 | g10780 | g10780.t1 | exon | g10780.t1.exon3 | 11913776 | 11914241 |
| chr_1 | g10780 | g10780.t1 | cds | g10780.t1.CDS3 | 11913776 | 11914241 |
| chr_1 | g10780 | g10780.t1 | TSS | g10780.t1 | NA | NA |
| chr_1 | g10780 | g10780.t1 | TTS | g10780.t1 | NA | NA |
Sequences
>g10780.t1 Gene=g10780 Length=1764
ATGCAGAGTGATTTATTTTCAGCTGCAAATGAAATAATATCATCCCAAAAGAAAGTAACT
GCATTGAACTTTATCATTGCTTTCAATAATGAGACAATTGAGAAAAAGTATGGAACATTG
ATAAATGATTTGATAGTGAAATCAAACAATTGTGTGATTTATATTGAACATGCGGACTTT
ATCAGTCAACGTAATCGACTCTTCAATGTTTTTATTGTGGACAATTTCAAATCCTTTAAT
CGCATATACAGTAGAATATCTTCGGATACATTCGTGATTGATGGCCTCTATCTCATTATT
TTCATTGAAAATATCAGCATGTCCGATATTGAACAGGCTACAAGACTCTTATGGGATCTA
TTCATCTACAATGTTAACTTTCTTCTTAAGGACAGTGGTGAAATCAACCTCATAACTTTT
ATGCCCTTCACGAAAGAAATGAATTGTGGAAATACGAGACCGAAAATAATTAATCAGTAT
GTTAACGGATCATTTTGGTCTGAAGTTCAGTACTATCCAGAAAAATTAACTAATTTGTTT
CAATGTCCAGTAAAAGTAGTGACATTCAATGCTCCACCTATGATGATGATAAAGTACTCA
GATGATTCATTTCAGTTATATGGAGTTGATGGTGAAATGATGACTGCACTAGCAAAAGAA
TTGAATTTTAAAATTGATGTACATCACATTTCTGACTTAATTAGATGGGGTTCATTAGTG
AATGGAACTAGTACTGGAGCCATGCGAATGGTCATCAACAATGAAGTAGATCTCACAGTT
GGGATGTATACAATTACATACCAAAGGTCAAAATTAATGACAAGCTCTGAATTTTACTAC
TCAGTTCCATTTATTCTAATTGTACCACCAGGATCAACTTTAACTTCATTAGAAAAACTT
TTCAGACCATTTCAGTTGCACGTTTGGATTCTTTTGCTCCTGATTTTTGTCATTGCTTTC
ATTACTGTGATTATAATAAGATTTCAAAGTAAATCAGTTCAAGATTTTGTATTTGGTAAA
AATAACAGGTCGCCTATATTAAATATTTTAAATGGTTTTCTTGGCAGCACACAAACAATT
TTACCAAAACGCAATTTTGCACGATATTTGCTCATAACGTATTTATTGTTTTGTTTGGTA
AAGAGATCACTTTATCAAGGTGCACTTTTTCAATTTCTGCAAAAAGATGAACAAAAAAGT
GAAATACAATCAATAGATGAGTTAGTTGAAAAAGGTTTTAAAGTTTATATGCTTCCATCT
TCATTGGAACATACTCAAAATATGAAATTCAAAAATCAACGACGAGCAGTAAATTCAACA
GTTTTATCAGAAAAACGTTTGGAGACATTAAATCCATTGTCGCAGCATGCCGTATCAAGT
TCCCTTGAGCAAATTCTTTACTACAACAAATTGAATTACAAAAACAACACATTGACAGTG
TGTCGAGAGTATCTCTTTACATTTCAGTATGGCATTTATTTTCGCAAAAATTCTTATCTT
ACAAAAATGTTCAACAAAAAAATTTCACTTTTTAAGACAGCTGGATTAATTGACTATTGG
TCATCAGATTTCATTAGCAATAAATACCTTAATATGAAAATCGATAGTGATGGTCCGAAG
AAATTAAATATGGAACACTTGTTGGGTAGCTTTGAACTACTTGCTGCAGGCGCTCTAATT
ACCATCATCATTTTCATATTTGAAATTTTAGCTGTTAAATTTAGGATTAAATCAATGCAA
ATGTTTTTCGAGTTTTTTGTATAA
>g10780.t1 Gene=g10780 Length=587
MQSDLFSAANEIISSQKKVTALNFIIAFNNETIEKKYGTLINDLIVKSNNCVIYIEHADF
ISQRNRLFNVFIVDNFKSFNRIYSRISSDTFVIDGLYLIIFIENISMSDIEQATRLLWDL
FIYNVNFLLKDSGEINLITFMPFTKEMNCGNTRPKIINQYVNGSFWSEVQYYPEKLTNLF
QCPVKVVTFNAPPMMMIKYSDDSFQLYGVDGEMMTALAKELNFKIDVHHISDLIRWGSLV
NGTSTGAMRMVINNEVDLTVGMYTITYQRSKLMTSSEFYYSVPFILIVPPGSTLTSLEKL
FRPFQLHVWILLLLIFVIAFITVIIIRFQSKSVQDFVFGKNNRSPILNILNGFLGSTQTI
LPKRNFARYLLITYLLFCLVKRSLYQGALFQFLQKDEQKSEIQSIDELVEKGFKVYMLPS
SLEHTQNMKFKNQRRAVNSTVLSEKRLETLNPLSQHAVSSSLEQILYYNKLNYKNNTLTV
CREYLFTFQYGIYFRKNSYLTKMFNKKISLFKTAGLIDYWSSDFISNKYLNMKIDSDGPK
KLNMEHLLGSFELLAAGALITIIIFIFEILAVKFRIKSMQMFFEFFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g10780.t1 | Gene3D | G3DSA:3.40.190.10 | - | 207 | 540 | 2.3E-43 |
| 12 | g10780.t1 | Gene3D | G3DSA:3.40.190.10 | - | 283 | 490 | 2.3E-43 |
| 10 | g10780.t1 | Gene3D | G3DSA:1.10.287.70 | - | 292 | 568 | 2.3E-43 |
| 3 | g10780.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 134 | 575 | 1.5E-79 |
| 4 | g10780.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 134 | 575 | 1.5E-79 |
| 1 | g10780.t1 | Pfam | PF00497 | Bacterial extracellular solute-binding proteins, family 3 | 190 | 518 | 1.9E-11 |
| 2 | g10780.t1 | Pfam | PF00060 | Ligand-gated ion channel | 519 | 557 | 4.5E-8 |
| 15 | g10780.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 277 | - |
| 19 | g10780.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 278 | 294 | - |
| 17 | g10780.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 295 | 305 | - |
| 21 | g10780.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 306 | 326 | - |
| 14 | g10780.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 327 | 365 | - |
| 18 | g10780.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 366 | 385 | - |
| 16 | g10780.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 386 | 552 | - |
| 20 | g10780.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 553 | 572 | - |
| 13 | g10780.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 573 | 587 | - |
| 9 | g10780.t1 | SMART | SM00918 | Lig_chan_Glu_bd_2 | 193 | 253 | 0.0089 |
| 8 | g10780.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 183 | 526 | 7.85E-31 |
| 7 | g10780.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 306 | 328 | - |
| 5 | g10780.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 366 | 385 | - |
| 6 | g10780.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 550 | 572 | - |
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:0015276 | ligand-gated ion channel activity | MF |
| GO:0004970 | ionotropic glutamate receptor activity | MF |
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