General information for g4068.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4068 is located on chr_3: 30340828..30350350 (+ 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 | g4068 | g4068.t1 | isoform | g4068.t1 | 30340828 | 30350350 |
| chr_3 | g4068 | g4068.t1 | exon | g4068.t1.exon1 | 30340828 | 30340945 |
| chr_3 | g4068 | g4068.t1 | cds | g4068.t1.CDS1 | 30340828 | 30340945 |
| chr_3 | g4068 | g4068.t1 | exon | g4068.t1.exon2 | 30348439 | 30349744 |
| chr_3 | g4068 | g4068.t1 | cds | g4068.t1.CDS2 | 30348439 | 30349744 |
| chr_3 | g4068 | g4068.t1 | exon | g4068.t1.exon3 | 30349894 | 30350350 |
| chr_3 | g4068 | g4068.t1 | cds | g4068.t1.CDS3 | 30349894 | 30350350 |
| chr_3 | g4068 | g4068.t1 | TSS | g4068.t1 | NA | NA |
| chr_3 | g4068 | g4068.t1 | TTS | g4068.t1 | NA | NA |
Sequences
>g4068.t1 Gene=g4068 Length=1881
ATGGACATATCAAGAGGAGGAAACAGCAATAGTAATAGCAATAATAGCATCAATACTATA
AGCAAAAGCACAATATTTCCTTTTCCAAGCCGAGTTGAAGGTTTCTTGGAATGCTGTGTC
GTGAATGTAATTACTGAAATTTGTGGCTACGATAAAAATACTGCGAGTGTAATATTTGAG
TCAAAGTGTTTAAGTAATTTTACATTTATGGATGATGTAAATCAAATTTTATTTGAAAGT
TTACAAAGCCAAAAAATTTCTCTACAGATCGAAACAGAAACTTTAAAACGTAATTCCTTA
CCAAATATCGAACGCTGTAATGTCATAATGATAAGCTCATGCAGTAGTTTTATGCGAATT
TATGAGTCACTTGCTGACAACGTTTTAACGCAACATTCTTCACCACTCCTAATCATTTTA
TATGATTACTATCAGTTTAAATTTCTTAATGAAATTTTTAGCACTTTATGGCGTGCAAAT
ATCTATAAAGTTAATGCATTGCTACTCAATGATGACAACACTGGTGTGTTAGTAATGTCA
TTCTTTCCATTTAGTGGATTACAATGCAACAATACTCGACCAGTTCTTATCAATCAATTT
ATTAATAAAAGCTTCATTCGACCAATTCAACTTTTTTTTCCTAAAAAGATGAGAAATCTT
CATCAATGTCCAATTCGTATTTCAACTTCAAATAATTCCGAGCCATATATTTTTGCTAAA
AAATTATCAGATGAAAATTATGAGTTACAAGGAAGAGAAATAAAATTACTCCATGGACTC
TCGGAAGCATTAAATTTTTCAATAATGTTTACTTATATTGGTAGAGAAGGTGTACTTTTA
GAAAATGGAACAGCAGAAGGCGCATACAAGACACTTCTTGATGGTCAAAGTGATATTGCA
ATAGCTGATATGTGGCTAAAAGCAAATAGATTAAAATTTATTGATGCTACAGATTCTTAT
ATTACTTCAACAATCATTTTTGTAATTCCACCTGGAGCAGAATTGACATCGTTTCAAAAA
TACTTTCAACCTCTTGATGCTTATACTTGGATGTTTCTTTTAATAATAATTGCTTTAGCC
TTTATTACAATTAAAACTGTCAAAGGATTGTCAATAGAAATTCAAGAATTTTTATTCGGT
AAAAATGTCCAAGATCCATATTTGAATGTCCTTGTTGCTGTTGTTGGCTTGTCACAACCA
GTTCTACCACGTAAAAATTTTGCTCGCTTCATGCTCATGATGTTTTTGCTCTTCTGTCTT
GTCATGAGATCCCTCTACCAAGGTTCGCTTTATCGCTTCTTACAGACAAATATGAGAAAT
AAGGAAGTGCAATCAATTGATGAAATGATTGAACGAGATTACAAATTTTATTTAGTACCA
TCGATTCTCGATTTATTCGAAGGTCAACCTAGAATTTATGAAAGAAAAATTGTTATGCCA
TTAGAACAACGAACATTGTTATTTAAAAAGTCTCTCGATCCTTCCTTTGATGGCGTTTTT
CCACGTTCACTAACTGGTGTGATGTATTCAAATCAGCTTAATTACAACACCTCAGTTTAT
TTGATTTGTAAGGAGAAATTTATGACATTCTCTATTGTGATTTATACTCGAAAGGGCTTC
TTTTTACTCAATGCACTGAATGACAAAATAGCGCAATTGCAAACAGCTGGTCTGATTGAT
TACTGGCACTCACAGATATTCGATCAACGCTATTTAAACATTAAAGAATCACAAGAGCCA
AAACCAACAGAATTGCATCATTTATCCGGTTGCTTTTGGCTCTTAATTATTGGTTGCACT
ACTGGTCTCGTGTCGTTTGTTTGTGAAATTTTATATGCAAAAATATTTGCAAGATCTCCC
AGCAGTAGCAAGCAGAAGTAA
>g4068.t1 Gene=g4068 Length=626
MDISRGGNSNSNSNNSINTISKSTIFPFPSRVEGFLECCVVNVITEICGYDKNTASVIFE
SKCLSNFTFMDDVNQILFESLQSQKISLQIETETLKRNSLPNIERCNVIMISSCSSFMRI
YESLADNVLTQHSSPLLIILYDYYQFKFLNEIFSTLWRANIYKVNALLLNDDNTGVLVMS
FFPFSGLQCNNTRPVLINQFINKSFIRPIQLFFPKKMRNLHQCPIRISTSNNSEPYIFAK
KLSDENYELQGREIKLLHGLSEALNFSIMFTYIGREGVLLENGTAEGAYKTLLDGQSDIA
IADMWLKANRLKFIDATDSYITSTIIFVIPPGAELTSFQKYFQPLDAYTWMFLLIIIALA
FITIKTVKGLSIEIQEFLFGKNVQDPYLNVLVAVVGLSQPVLPRKNFARFMLMMFLLFCL
VMRSLYQGSLYRFLQTNMRNKEVQSIDEMIERDYKFYLVPSILDLFEGQPRIYERKIVMP
LEQRTLLFKKSLDPSFDGVFPRSLTGVMYSNQLNYNTSVYLICKEKFMTFSIVIYTRKGF
FLLNALNDKIAQLQTAGLIDYWHSQIFDQRYLNIKESQEPKPTELHHLSGCFWLLIIGCT
TGLVSFVCEILYAKIFARSPSSSKQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4068.t1 | Gene3D | G3DSA:3.40.190.10 | - | 248 | 581 | 1.9E-38 |
| 12 | g4068.t1 | Gene3D | G3DSA:3.40.190.10 | - | 324 | 532 | 1.9E-38 |
| 10 | g4068.t1 | Gene3D | G3DSA:1.10.287.70 | - | 334 | 609 | 1.9E-38 |
| 3 | g4068.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 107 | 619 | 8.6E-66 |
| 4 | g4068.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 107 | 619 | 8.6E-66 |
| 2 | g4068.t1 | Pfam | PF10613 | Ligated ion channel L-glutamate- and glycine-binding site | 227 | 329 | 8.4E-10 |
| 1 | g4068.t1 | Pfam | PF00060 | Ligand-gated ion channel | 399 | 599 | 3.3E-8 |
| 16 | g4068.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 346 | - |
| 17 | g4068.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 347 | 364 | - |
| 14 | g4068.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 365 | 406 | - |
| 18 | g4068.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 407 | 426 | - |
| 15 | g4068.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 427 | 591 | - |
| 19 | g4068.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 592 | 617 | - |
| 13 | g4068.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 618 | 626 | - |
| 9 | g4068.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 222 | 563 | 4.68E-19 |
| 6 | g4068.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 347 | 364 | - |
| 5 | g4068.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 385 | 402 | - |
| 7 | g4068.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 412 | 434 | - |
| 8 | g4068.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 591 | 613 | - |
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