General information for g12623.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g12623 is located on chr_1: 24824805..24826687 (- 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 | g12623 | g12623.t1 | isoform | g12623.t1 | 24824244 | 24826687 |
| chr_1 | g12623 | g12623.t1 | exon | g12623.t1.exon1 | 24824244 | 24824805 |
| chr_1 | g12623 | g12623.t1 | cds | g12623.t1.CDS1 | 24824244 | 24824805 |
| chr_1 | g12623 | g12623.t1 | exon | g12623.t1.exon2 | 24824859 | 24825747 |
| chr_1 | g12623 | g12623.t1 | cds | g12623.t1.CDS2 | 24824859 | 24825747 |
| chr_1 | g12623 | g12623.t1 | exon | g12623.t1.exon3 | 24826225 | 24826687 |
| chr_1 | g12623 | g12623.t1 | cds | g12623.t1.CDS3 | 24826225 | 24826687 |
| chr_1 | g12623 | g12623.t1 | TSS | g12623.t1 | NA | NA |
| chr_1 | g12623 | g12623.t1 | TTS | g12623.t1 | NA | NA |
Sequences
>g12623.t1 Gene=g12623 Length=1914
ATGAACATAAAATTTATTTCACTTATCATTCTAATAACTCATGCAGAGTTAATTCACTGT
GAAATTAATGACGCAGTACGAGCAGTAAGCGATGCAATTGTAATGACAGAAATTCATGAA
ATCAGTTTAATTGCCGATTTGCAAAATTCTCATGTTGAAAAGTTGATAAAACTTTTGCAT
AGTAAAACCACTTTAAGTTTGACTATCGAAAATCTTCATGAAAGCAAAGCAAAGAGATTA
TCGACATTGAATGTCCTCATAACCGAGAAAAATGAATCATTAAGTGAATTATTTTCTCAA
AACTTTGGCATTTCGAGAAAGTTTTTCCTATTGATTTTCTTCAATGATGACAACGATAAT
GATGACGATGGAAACGAGAAAGCTTTGAAAGTTTTCAACGAGTTTTGGAAATTCAGCATC
TACAATGTTAATATTATTATTCTGAGCGCAGAAAACTGTGAAGATCATATAAAAATGTTG
ACATTCATGCCATTTTCATCGCATGGTTGCAGCAACTTGATTCCAATAACAATCAATAAA
TTTTATTGCAACAATCACTCGTGGTCATATCACAATGAACAAGTTTTTCCACAGAAATTC
AAGAATCTTTTTGAATGTCCCATTAAAGTGTCAACATTCAACCTTCCACCGAGTATTATT
GTTGACAAGGGTGAGAATGGCACGAGCCATCGTTTGCGAGGACATGAAATTGAATTATTG
AATGGATTGTCAGAAATGCTGAAATTTAAATTGAATTTTGAAATACGTACGGAAGCAGCT
GCGTGGGGGCAAATATTTGAAAATGGAACTGCAACGGGCGTATTAGGCCGAATTGTGAAT
GCTCAAGTTGACATTGGAATCGGAACTTATTATTTGACTTTTACTCGTGCAAAATTCATG
AGTTTCATTCAGTACAGCAGTTCTAAAATAATTTTAACAGTTCCAAGGGCATTACCGCTC
TCATCACTCGAAAAACTCATTGCTCCACTAACCGCAGCTACGTGGATTGTTTTATTGCTG
CATTTGTGTATTGGATTTGTTGCAATTTCATTAATGCAAAAATTGAAATTTGAACTGCAA
AGCTGTCCGCACATGAATATGCTAAATATTCTTTTTAATGGCTCACAGCATGTTGTACCA
CGTTCTGTGCCATTGAGATTAATTTTATGGTCTTTTGTAATGTTTTGTTTAATCATTCGA
ACACTCTATCAAGCGGGATTGTTTAAATTTTTACAGTCAGATCAACGTCACAATGAATTG
CAAAATATTGATGAAGTTATTGAGAAGAATTTTGATATTTTTATGTATGAATCATTTCAA
GAACTCAGTAAAGGATTGAAAATTCATCAAAACCGAAAACTCGTCAAAAATAACGAAACA
ATTGAATTTTACCAAATGCAAACATTAAATCCAAAATTTAAAGGAGCAGCTGTTGGTCCA
CTTTATGAAATCATCTATGCAAATCAACTAAATTACAAAAATTTCACATTCAAAACTTTA
CCAGAGATAATTTTTGCACTTCCTGTTGCTATGTATCTACCAAAAAATCATTTTTTGAAG
AGTGAAATTGAATATTGTGTTGGATTTTTACATGCCAGTGGTTTGATTGATTACTGGCAG
AAACAATATTTGAATGACTTCTATTTAAAGATTGATACAATCAATGATGAACCAAAAATA
CTGACATTCTCACATCTGTCTGGTATTTTTTATATTTGGATTGGTTGCTGCTGTGCTTCA
ATTTTATGCTTTTTCTTCGAAATAATTTGGAAAAAAATTGAAAATTTTAGAAACGGGAAA
AATCAAAATTTTGAGAAAATTAATGAAAATGTAAATAAAAATCATGAATATCATTTCTTA
TTTTATGAAATAATTAAGGAAAAACAAAGAGCAAAATTTTTGATAAAAAAATAA
>g12623.t1 Gene=g12623 Length=637
MNIKFISLIILITHAELIHCEINDAVRAVSDAIVMTEIHEISLIADLQNSHVEKLIKLLH
SKTTLSLTIENLHESKAKRLSTLNVLITEKNESLSELFSQNFGISRKFFLLIFFNDDNDN
DDDGNEKALKVFNEFWKFSIYNVNIIILSAENCEDHIKMLTFMPFSSHGCSNLIPITINK
FYCNNHSWSYHNEQVFPQKFKNLFECPIKVSTFNLPPSIIVDKGENGTSHRLRGHEIELL
NGLSEMLKFKLNFEIRTEAAAWGQIFENGTATGVLGRIVNAQVDIGIGTYYLTFTRAKFM
SFIQYSSSKIILTVPRALPLSSLEKLIAPLTAATWIVLLLHLCIGFVAISLMQKLKFELQ
SCPHMNMLNILFNGSQHVVPRSVPLRLILWSFVMFCLIIRTLYQAGLFKFLQSDQRHNEL
QNIDEVIEKNFDIFMYESFQELSKGLKIHQNRKLVKNNETIEFYQMQTLNPKFKGAAVGP
LYEIIYANQLNYKNFTFKTLPEIIFALPVAMYLPKNHFLKSEIEYCVGFLHASGLIDYWQ
KQYLNDFYLKIDTINDEPKILTFSHLSGIFYIWIGCCCASILCFFFEIIWKKIENFRNGK
NQNFEKINENVNKNHEYHFLFYEIIKEKQRAKFLIKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12623.t1 | Gene3D | G3DSA:3.40.190.10 | - | 231 | 559 | 3.1E-35 |
| 7 | g12623.t1 | Gene3D | G3DSA:3.40.190.10 | - | 309 | 509 | 3.1E-35 |
| 6 | g12623.t1 | Gene3D | G3DSA:1.10.287.70 | - | 319 | 587 | 3.1E-35 |
| 2 | g12623.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 76 | 601 | 1.4E-70 |
| 3 | g12623.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 76 | 601 | 1.4E-70 |
| 1 | g12623.t1 | Pfam | PF10613 | Ligated ion channel L-glutamate- and glycine-binding site | 209 | 304 | 2.3E-8 |
| 13 | g12623.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 14 | g12623.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 15 | g12623.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 12 | - |
| 19 | g12623.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 20 | - |
| 12 | g12623.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 325 | - |
| 17 | g12623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 326 | 351 | - |
| 9 | g12623.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 352 | 382 | - |
| 16 | g12623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 383 | 403 | - |
| 11 | g12623.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 404 | 569 | - |
| 18 | g12623.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 570 | 590 | - |
| 10 | g12623.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 591 | 637 | - |
| 23 | g12623.t1 | SMART | SM00918 | Lig_chan_Glu_bd_2 | 217 | 280 | 3.4E-4 |
| 4 | g12623.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 207 | 544 | 2.5E-19 |
| 5 | g12623.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 21 | g12623.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 327 | 349 | - |
| 20 | g12623.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 382 | 404 | - |
| 22 | g12623.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 568 | 590 | - |
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. There were no conditions that were differentially expressed