General information for g4066.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4066 is located on chr_3: 30331251..30333069 (- 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_3 | g4066 | g4066.t1 | isoform | g4066.t1 | 30331251 | 30333069 |
| chr_3 | g4066 | g4066.t1 | exon | g4066.t1.exon1 | 30331251 | 30331642 |
| chr_3 | g4066 | g4066.t1 | cds | g4066.t1.CDS1 | 30331251 | 30331642 |
| chr_3 | g4066 | g4066.t1 | exon | g4066.t1.exon2 | 30331701 | 30331768 |
| chr_3 | g4066 | g4066.t1 | cds | g4066.t1.CDS2 | 30331701 | 30331768 |
| chr_3 | g4066 | g4066.t1 | exon | g4066.t1.exon3 | 30331826 | 30333069 |
| chr_3 | g4066 | g4066.t1 | cds | g4066.t1.CDS3 | 30331826 | 30333069 |
| chr_3 | g4066 | g4066.t1 | TSS | g4066.t1 | NA | NA |
| chr_3 | g4066 | g4066.t1 | TTS | g4066.t1 | NA | NA |
Sequences
>g4066.t1 Gene=g4066 Length=1704
ATGTCGCACATCGATTTTGGTTTATGCAAATTACTAACGACCTTACCAGAGAAAGACGAT
AAAATGATTAATATCATATTTGGTCAGACGAGGAGCAACTTTGAATTTCTAAAATGTTTT
ACAATTCCCATAGCAATCGAAACAATAGATAGTTTGAAAGATATTGGCTACAAAAGAGAC
TTTAATTTGATATTCATTGATAACGACAAAGACGATTTGAGGAAATTTCATGATAGATTT
TCATCAAAATTATTTAATAGTCGTGGTCGTTATATTATAATTGCTAATGATGTTGACAAA
AATATTTTTAAATGGTTTTGGGATAAACAAATATTAAATGTGAATATCATCAGTAAGGGA
CCAAATGGGAATTTGATTGTGCTCACATATTTTCCATTCAAAAATTATGATTGCGGCAAT
ACACAACCAACTGTCATTAACATTTCGATAATTACTCAATTCTTTCCAGATAAACTTATA
AATTTACAAAATTGTAAAATACGACTTGCAACTTCAAAAATTTCTGAGCCTCATGTTAAT
TTTATAAAAGACAGCAATGGAACTATAATTCGACTTTATGGTCGAGACATTAATCTTATC
AATACATTATCGCAAGCAATAAACTTTGACGTTGATATAGTTTATGTGGGAATCGAAGGT
GCGTTGTGGAATAATGGAAGTGCTGAGGGTCCCTTTAAATTTTTACTTGATAACAAAGCT
GATTTAATCGTTGCTGATTATTGGTTGATGCCAACCAGATTAAAATTTATTGATAGTACT
CTTCCTTATGCTGCACAGCACATTGCTTTCATAATTCCTCCTGGTGCTTCATATTCTCCA
TTTAGAAAACTAATTATGCCATTTGACGCATGCACATGGACTGTCTTAGTCTTGATATTC
CTAATTAGTTTTATTGTCATATTTGGAGCAACAAAAATTCGCTTTTTTGGCATATCGATA
TCGTCTGCTGACCCATATATGAATATAATTAGAGCTATTCTCGGCGGAACTCAAAATGCT
CTGCCAAAAAGAAACTCAAGTAGAATTTTGCTAATGGCATTTTTGATTTTATTTCTTGTA
ATGAGAACGCTCTATTTGGCATCATTTTATCAGTATATGCAAAAAAATATTATGTACAAA
GAGGCTCAATCGATCGATGACATGGTTGAACGAGATTTTACAATTTATTATTTGACATCA
TTTGAAGATCTTATGGAAGGTGCACCATTAAAATTGAAGAATAGGCTTGTTGGGTTAACA
ATTGCTCAGCGTGCAAAAATATTGCCACTAGTCTATAATCCTTCTTTTAAAGGTGCATTC
TTGAGATCACTTACTGGCATTCAGTATTTAAATCAATACAACTATAACAAAAATAAAACA
ACAGCAAAAATGTTTATGATCTGTAAAGAATATTTTATGACAATTCCAGTTGTGATTTAT
ACAAAAAAGGATTTTTATCTTGTCAATAAAATCAACGAGAAAATTCAACTCATGCAAGCA
GCAGGTTTGATTGATTACTGGCACTCGCAATCAATCGATAGAAAGTATGAGAAAATTGCT
GCTTCTGCAGCCCAGCCTATTAAATTAAGCTTTAATCATTTATTAAGTTGCTTTACTATT
TTGATATGTGGATTAATTATTTCATTAATTATCTTTATAGCTGAGAATTGCAAATTTTGG
CTGATGAGAATAAGAAATGGCTAG
>g4066.t1 Gene=g4066 Length=567
MSHIDFGLCKLLTTLPEKDDKMINIIFGQTRSNFEFLKCFTIPIAIETIDSLKDIGYKRD
FNLIFIDNDKDDLRKFHDRFSSKLFNSRGRYIIIANDVDKNIFKWFWDKQILNVNIISKG
PNGNLIVLTYFPFKNYDCGNTQPTVINISIITQFFPDKLINLQNCKIRLATSKISEPHVN
FIKDSNGTIIRLYGRDINLINTLSQAINFDVDIVYVGIEGALWNNGSAEGPFKFLLDNKA
DLIVADYWLMPTRLKFIDSTLPYAAQHIAFIIPPGASYSPFRKLIMPFDACTWTVLVLIF
LISFIVIFGATKIRFFGISISSADPYMNIIRAILGGTQNALPKRNSSRILLMAFLILFLV
MRTLYLASFYQYMQKNIMYKEAQSIDDMVERDFTIYYLTSFEDLMEGAPLKLKNRLVGLT
IAQRAKILPLVYNPSFKGAFLRSLTGIQYLNQYNYNKNKTTAKMFMICKEYFMTIPVVIY
TKKDFYLVNKINEKIQLMQAAGLIDYWHSQSIDRKYEKIAASAAQPIKLSFNHLLSCFTI
LICGLIISLIIFIAENCKFWLMRIRNG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4066.t1 | Gene3D | G3DSA:3.40.190.10 | - | 192 | 527 | 3.1E-34 |
| 10 | g4066.t1 | Gene3D | G3DSA:3.40.190.10 | - | 267 | 477 | 3.1E-34 |
| 9 | g4066.t1 | Gene3D | G3DSA:1.10.287.70 | - | 277 | 555 | 3.1E-34 |
| 2 | g4066.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 89 | 555 | 1.7E-52 |
| 3 | g4066.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 89 | 555 | 1.7E-52 |
| 1 | g4066.t1 | Pfam | PF10613 | Ligated ion channel L-glutamate- and glycine-binding site | 171 | 272 | 1.2E-8 |
| 14 | g4066.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 291 | - |
| 17 | g4066.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 311 | - |
| 13 | g4066.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 312 | 348 | - |
| 16 | g4066.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 349 | 370 | - |
| 15 | g4066.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 371 | 532 | - |
| 18 | g4066.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 533 | 554 | - |
| 12 | g4066.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 555 | 567 | - |
| 8 | g4066.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 163 | 508 | 1.19E-20 |
| 6 | g4066.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 286 | 308 | - |
| 7 | g4066.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 315 | 334 | - |
| 4 | g4066.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 349 | 370 | - |
| 5 | g4066.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 531 | 553 | - |
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