General information for g12735.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12735 is located on chr_1: 25519768..25521685 (- 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 | g12735 | g12735.t1 | isoform | g12735.t1 | 25519768 | 25521685 |
| chr_1 | g12735 | g12735.t1 | exon | g12735.t1.exon1 | 25519768 | 25520269 |
| chr_1 | g12735 | g12735.t1 | cds | g12735.t1.CDS1 | 25519768 | 25520269 |
| chr_1 | g12735 | g12735.t1 | exon | g12735.t1.exon2 | 25520322 | 25521685 |
| chr_1 | g12735 | g12735.t1 | cds | g12735.t1.CDS2 | 25520322 | 25521685 |
| chr_1 | g12735 | g12735.t1 | TSS | g12735.t1 | NA | NA |
| chr_1 | g12735 | g12735.t1 | TTS | g12735.t1 | NA | NA |
Sequences
>g12735.t1 Gene=g12735 Length=1866
ATGAACGTGTTTATGATTCTATTTGCAAGTTTATTCGTGTCAATTAGGTGCGACAAATCA
AAAATTTTACAAAATAAACAACGTGATGAACTTATGGAAGCATTTTTCGAAGCTTTTTTG
TTGTCTGCAAATTTTAGTGCGCGAATTATTGGTAGAACAGAACTTTTTGAGCAAACTGAA
TTCTCTTCATTGCATGTTCCTTACGAACTTTGGTGCACTGACTTTTTTACAGCAAATAAA
ACGGAAATCAACTCACTTTCACCGTCATTTATCAATTCAGTTTTATTTGCCAACAATCAA
GAAATTTTTACAATATTTTCGAGGGAGAATTTGAAATTCTTTCGACTTGATGGTTTTTAT
ATGCTCCTTTCATATAGTGAATGCTCAAAAAATGATGATAAAATCTTTGAACATTTGTGG
AAACGGCAAATTTTTAATGTCAATTTAATTTGCAAACTCAATATGGAAATCTTCATGACA
ACTTTTTTCCCTTATCAAAATAGCAGCTGCGGAACCATAAATTCTCTCGTAATTAACAAA
TTTTCAAATCATTCATGGATTAACAAAGTGATTTTCCCTGAGAAATTTAAAAATCTCTAC
AACTGCCAGCTACGAGTTGCTTCTTTTTATTATTCACCAATAACAATGCGTGAAGATTTA
GGTAATGGAACTTTTCGATATTATGGCAGTGAAATGGAAATTTTGTCAGGATTAGCGGAG
GCGCTTAATTTTCAAATCAATCATAATTATGTGCCAGCCTCTGGTATGGCTGGTATTTTA
TTAGAAAATGGCACATCTACGGGATTATTAAAGCAAACAATCGAAGGTGAAATGGATATG
CTTATGGGTTTCTACTATCTAACTTATCTACGAACTAAATTCCTTAGTTTTTCACAATCT
CATTATAGTGTTCCGTTAGTGATAATGATTCCACTCGGGAAACCATATACACCTTTCGAA
AAACTTTTTAATCCATTGCAGTTCATGGTATGGATTTTTCTACTGATAACAATTATTCTT
GGTTTGGCCTGCATTGGTGTTGTGAATTGTCAGAATGATAAAATTAAAAATTTTGTTTTT
GGAAAAGACATCAGAGATCCTTATATGAATTTTTTAAACATTCTTTTAAATGGTTTTCAA
ACAAAGTTGCCAAAGCGAACTTTTGCACGAACTATACTGATGATGTTCATGATGTTTTGC
TTTATTTTAAGAACTCTTTATCAAGGTTCACTTTTTCAATTTCTTCAATCAGATGATAGA
AATCCTGAAATGGCTACAATTGATGAAATGATTGAAAAAAATTGTATCTTTTATGTTCGT
GAGACACTTGAGCATAACATTAAAAATATGAGCTTTTATAAAAAACGAAAAGTTGTAAAA
TATGCTGAGTATCCAGCTTTGATTAAAAGAACTCGTGATTCAGATTTTAATGGAGGAATA
ATAATGCCGCTTCTTGAAGTCATTACAGCAAACCAACAAACTTATAGAAACTATACCTAC
AAAGTTTTAAAAGAATATCTCTTTGATGTGCAGATTGTTTGCTATTTTCCAAAAAACTTT
CATTTAATTGACATTATCAATGAAAAAATTGCAATACTTAAAGCTGCTGGATTAATTTCA
ATGTGGATGGACAAATATGTTGATAAAACTTTTATTAATATTAAACCAGATACACCTGGA
CCTAAGAGACTTAATATTGAACATCTTTATGGTGGATTTGAACTTTTATTTTATGGAATT
ATTATATCAGTTATTGCTTTCTTCATTGAAATTATCAATGCGAATATTTCAGTAAAATTA
TTTAAGAACAAAAGTGTGAATAAGAAAAATAAGACTAGAAGACAATTGTTCACTTATTTA
GATTAA
>g12735.t1 Gene=g12735 Length=621
MNVFMILFASLFVSIRCDKSKILQNKQRDELMEAFFEAFLLSANFSARIIGRTELFEQTE
FSSLHVPYELWCTDFFTANKTEINSLSPSFINSVLFANNQEIFTIFSRENLKFFRLDGFY
MLLSYSECSKNDDKIFEHLWKRQIFNVNLICKLNMEIFMTTFFPYQNSSCGTINSLVINK
FSNHSWINKVIFPEKFKNLYNCQLRVASFYYSPITMREDLGNGTFRYYGSEMEILSGLAE
ALNFQINHNYVPASGMAGILLENGTSTGLLKQTIEGEMDMLMGFYYLTYLRTKFLSFSQS
HYSVPLVIMIPLGKPYTPFEKLFNPLQFMVWIFLLITIILGLACIGVVNCQNDKIKNFVF
GKDIRDPYMNFLNILLNGFQTKLPKRTFARTILMMFMMFCFILRTLYQGSLFQFLQSDDR
NPEMATIDEMIEKNCIFYVRETLEHNIKNMSFYKKRKVVKYAEYPALIKRTRDSDFNGGI
IMPLLEVITANQQTYRNYTYKVLKEYLFDVQIVCYFPKNFHLIDIINEKIAILKAAGLIS
MWMDKYVDKTFINIKPDTPGPKRLNIEHLYGGFELLFYGIIISVIAFFIEIINANISVKL
FKNKSVNKKNKTRRQLFTYLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12735.t1 | Gene3D | G3DSA:3.40.190.10 | - | 226 | 562 | 1.2E-37 |
| 10 | g12735.t1 | Gene3D | G3DSA:3.40.190.10 | - | 305 | 512 | 1.2E-37 |
| 9 | g12735.t1 | Gene3D | G3DSA:1.10.287.70 | - | 315 | 590 | 1.2E-37 |
| 2 | g12735.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 84 | 603 | 6.8E-64 |
| 3 | g12735.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 84 | 603 | 6.8E-64 |
| 1 | g12735.t1 | Pfam | PF10613 | Ligated ion channel L-glutamate- and glycine-binding site | 204 | 310 | 2.4E-7 |
| 16 | g12735.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 17 | g12735.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 18 | g12735.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 22 | g12735.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 17 | - |
| 15 | g12735.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 327 | - |
| 20 | g12735.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 328 | 348 | - |
| 13 | g12735.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 349 | 387 | - |
| 19 | g12735.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 388 | 407 | - |
| 14 | g12735.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 408 | 574 | - |
| 21 | g12735.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 575 | 601 | - |
| 12 | g12735.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 602 | 621 | - |
| 7 | g12735.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 202 | 549 | 9.68E-24 |
| 8 | g12735.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 4 | g12735.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 328 | 350 | - |
| 5 | g12735.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 388 | 407 | - |
| 6 | g12735.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 576 | 598 | - |
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: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.
