General information for g4067.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4067 is located on chr_3: 30333329..30335228 (- 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 | g4067 | g4067.t1 | isoform | g4067.t1 | 30333329 | 30335228 |
| chr_3 | g4067 | g4067.t1 | exon | g4067.t1.exon1 | 30333329 | 30333776 |
| chr_3 | g4067 | g4067.t1 | cds | g4067.t1.CDS1 | 30333329 | 30333776 |
| chr_3 | g4067 | g4067.t1 | exon | g4067.t1.exon2 | 30333838 | 30335228 |
| chr_3 | g4067 | g4067.t1 | cds | g4067.t1.CDS2 | 30333838 | 30335228 |
| chr_3 | g4067 | g4067.t1 | TSS | g4067.t1 | NA | NA |
| chr_3 | g4067 | g4067.t1 | TTS | g4067.t1 | NA | NA |
Sequences
>g4067.t1 Gene=g4067 Length=1839
ATGAAGTTATTTAATCTGCTTCTCTTTACTTGCATAATCTCAACAGCAGTAGCAAAAATA
AATATTGAGAATAAAAATTATTCACTTCTATCTAGTGCACTTTGTGAAGTTGTGGACAAA
GTACTTACTGATCTCGCTGTAACTTTAAATGTAGTTTCAATTAATAGCAATCACGAGAAT
AACGATTTTCGAGACAGTTTCGTAAAAGAGGTTACAAAAAATCCTTCAATGTTAATTCGA
CAACAGAAACTTGATAAATTAGAATCTCTTTATACAAGAGGTCCAAGAAAAACTAGTCTT
GTAGCACTTCAATCATTTGCAGATTTTATGAAATTTTATTCGGAAATTAATGATGAAAAT
TTTCTAACGCGTGGACTTTATATTTTTGTGCTTACAAATGGACGGTTTAGTGAGATTGAA
AAGATGTTTGAAGTCTTTTGGAAATTGCAAATGTACAATACTAATGTAATTTATGAGAGT
AATGACAGACTCTTGGTTGAGACATTCTTTCCATTCAGCTCACAAACAAATTGCTCAAAT
ACACAACCAGTCATCATCAATGAATACAAGCTGACAAGTTTCACATACGACATCAAAGAA
TTCTTTCCAAACAAAATGAATAATCTCAAAAAATGTACTGTTCGTGTCGCTACATCAAAC
ACTTCTGTGCCTTACATTTACATGAAGAAAATGTTTAATGGAGAGAAGCGTCTTTATGGA
CGAGATTATGATTTAATTGAAACACTGGCACAAACATTGAATTTTAGAATTAATTTTACA
TACATCGGTAGGGAAGGATATATGTTTACGAATAATACTGCAGGTGGAACGTTTTTGTTT
TTATTAAACAATAAAGCTGATTTGACAGTAGCAGATTACTGGCTCAAATCATATCGTTTA
AAATATTTTGATGCTTCAACACCATACATTAATGAAAAGCTTGTCTTTGTCATACCATTA
GGCAGTCAGTTGTCATCACTCGAAAAACTTCTTTATCCGTTGACATTTTCGACATGGATG
ACACTTATTGCTTGTTTTATTATCGGTTCTATTGTCATTTTTGTCATCAAACTTCAATCG
AAAACAATTCAGAATTTTGTGTTTGGAACTCGTGTGAAATATATATATTTAAACTTATGG
ATAGGACTTGTCGGAACACTTCAACATCGTCTACCAAGCAGAAATTTTTCAAGATTTATT
CTGACACTTTTTTTGATCTTTTGTCTTATTATTCGAACGGCATACCAAGGAAAAATGTAT
CAGTTTATGCAATCAAATAAGAAGCATTCTGAACCACAAACAATTAACGAAATGATTGAA
AGAAAATATACATTTACATTGCTTAATAATTATGCTGATCTTGTTATTGATAAGACACGT
TGGGGAATTGTTGACATGAAGCCTCTTGGATTAGATTTATTCCAATGGGCAAAACAAATA
AAAGGTGATGAGAAAAATACAATTTTATTGCCACATACTCAAGTCTATTACAAATTAATT
GTCAACAACACACGCAATTTGATGATTTGTAAGGAATATTTTATGACAATTCCAACTGTT
ATTTATACGATAAAAAATTTCTACTTGCTTAATGCAATAAACAGTCAAATTGAAGAATTT
AATTCAGCTGGATTGATTGAATATTGGCATTCATTAGCATTTGATAAAAAATATATGAAG
GCTGAAATTGACAAACAACCAAAAGTTCTCACTATCGCACATTTATCAGGAGTTTTTGAA
TTATTATTGTTTGGACTTATAATCAGCTTCATCACTTTCATTTTTGAATGTGTGCTTGCA
AAGTGGGAAAATTATAAAAAGCACGTTACTAAAGCATAA
>g4067.t1 Gene=g4067 Length=612
MKLFNLLLFTCIISTAVAKINIENKNYSLLSSALCEVVDKVLTDLAVTLNVVSINSNHEN
NDFRDSFVKEVTKNPSMLIRQQKLDKLESLYTRGPRKTSLVALQSFADFMKFYSEINDEN
FLTRGLYIFVLTNGRFSEIEKMFEVFWKLQMYNTNVIYESNDRLLVETFFPFSSQTNCSN
TQPVIINEYKLTSFTYDIKEFFPNKMNNLKKCTVRVATSNTSVPYIYMKKMFNGEKRLYG
RDYDLIETLAQTLNFRINFTYIGREGYMFTNNTAGGTFLFLLNNKADLTVADYWLKSYRL
KYFDASTPYINEKLVFVIPLGSQLSSLEKLLYPLTFSTWMTLIACFIIGSIVIFVIKLQS
KTIQNFVFGTRVKYIYLNLWIGLVGTLQHRLPSRNFSRFILTLFLIFCLIIRTAYQGKMY
QFMQSNKKHSEPQTINEMIERKYTFTLLNNYADLVIDKTRWGIVDMKPLGLDLFQWAKQI
KGDEKNTILLPHTQVYYKLIVNNTRNLMICKEYFMTIPTVIYTIKNFYLLNAINSQIEEF
NSAGLIEYWHSLAFDKKYMKAEIDKQPKVLTIAHLSGVFELLLFGLIISFITFIFECVLA
KWENYKKHVTKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4067.t1 | Gene3D | G3DSA:3.40.190.10 | - | 236 | 568 | 3.7E-35 |
| 8 | g4067.t1 | Gene3D | G3DSA:3.40.190.10 | - | 313 | 519 | 3.7E-35 |
| 7 | g4067.t1 | Gene3D | G3DSA:1.10.287.70 | - | 323 | 596 | 3.7E-35 |
| 2 | g4067.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 91 | 608 | 1.0E-70 |
| 3 | g4067.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 91 | 608 | 1.0E-70 |
| 1 | g4067.t1 | Pfam | PF10613 | Ligated ion channel L-glutamate- and glycine-binding site | 214 | 317 | 3.6E-9 |
| 15 | g4067.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 16 | g4067.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 17 | g4067.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 22 | g4067.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 14 | g4067.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 329 | - |
| 18 | g4067.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 330 | 354 | - |
| 11 | g4067.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 355 | 373 | - |
| 21 | g4067.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 374 | 391 | - |
| 12 | g4067.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 392 | 396 | - |
| 19 | g4067.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 397 | 415 | - |
| 10 | g4067.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 416 | 568 | - |
| 20 | g4067.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 569 | 595 | - |
| 13 | g4067.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 596 | 612 | - |
| 4 | g4067.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 210 | 551 | 1.02E-21 |
| 6 | g4067.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 23 | g4067.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 5 | g4067.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 18 | - |
| 24 | g4067.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 334 | 356 | - |
| 26 | g4067.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 396 | 415 | - |
| 25 | g4067.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 578 | 600 | - |
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