General information for g988.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g988 is located on chr_3: 7269634..7271579 (- 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 | g988 | g988.t1 | isoform | g988.t1 | 7269634 | 7271579 |
| chr_3 | g988 | g988.t1 | exon | g988.t1.exon1 | 7269634 | 7270129 |
| chr_3 | g988 | g988.t1 | cds | g988.t1.CDS1 | 7269634 | 7270129 |
| chr_3 | g988 | g988.t1 | exon | g988.t1.exon2 | 7270201 | 7271579 |
| chr_3 | g988 | g988.t1 | cds | g988.t1.CDS2 | 7270201 | 7271579 |
| chr_3 | g988 | g988.t1 | TSS | g988.t1 | NA | NA |
| chr_3 | g988 | g988.t1 | TTS | g988.t1 | NA | NA |
Sequences
>g988.t1 Gene=g988 Length=1875
ATGAGACCTTTTTGGATATTTTTTGTCCTTTTTATTTTATTTTCTTTAGTACAAGGGAAA
ATTGAAAGTTTAAATAATTTTCAACATCCATTAAGTAAAGCTACTGGAGATTTAATAGAA
AATGTCATAAAAGATTCTGAAATTCAAAATGTAAGAATCATCATGTTAATGAGCAATGAA
TCTTCATTAGAAAATGTTGATATTGGCAATGAAATTGTAAAAGTTGCAACAACAAAATTT
AAAATTCAAACAAGAGGAAATTTAAGACAACCAATAGATCGTGAGAAAAGAATTTCACCA
GTAATTTTAATGGTTGATTCAATTGGAACTTTTAATTTAAGTAAATTAAGAATTGAGCAT
GACACTCCCAAATTTTACTTAGTTATTCTAACTAAAGGAATTTTCAAAGAAATCATTGAA
ATTCTTGACTTTTTTTGGAAAAACTCTGTCAGTGATGTCAATTTCCTTGTGCTCAATCAA
ACAGTTGTCGAAATGTACACATTTTTTCCTTTTGCAAACAAAAAATGTGGCACTGACTTG
TCACTTGTGCTGATCAATACCTTTGACTTAACGACTTGCACGTGGAGTGGTAATCAATTT
TTTCCTAGTAAAATAAAAAATCTTCATAAATGTCAGATTAAAGTTGGAGTTTCTGTGAAT
GTTCCAATGGTTATTTTTAATAATAAAACAACGCAAAAATATGATGGAATTGAAGTTACT
TTAATAAGAGAAATTGCAAAAGAATTTGATTTTGTTCCGCAATTCACTAAACCATATGAA
AGTGTTGGAGCAATTAATTCTAATGGAAGTTCAAGTGGATTAATTAGTGAAGTTTATAAA
AGAAAACTTGATGTGGCAATTGGCTCATTATCGCTTCAAATTGATCGTACAAATTATTTA
TCAGCAACAACTTCATTTGCAACAGTTCCGATAGTTATTGTAATTCCACCAACTCCACAA
ATTTCACCATTTGCTAAACTTTATTTACCTTTTGATTTTACAACTTGGTCTTTACTCCTT
GCAATGTTTCTAATTGGATATATCGTGATTATTGTCACCAAATTATTTGCAAAAACTCTT
TATAAACTAATTGTTGGTAAAAATGTAAATTATCCATTTACCAACATGTTCATAGCATTC
TTTGGATTATCACAAAATGTTTTACCAAAAGCAAATTTTTCAAGATTTTTATTAGCTAAA
TTTTTAATTTTCTGTCTTGTTATTCGAGGACTTTATCAAGGAAAATTATTTGATATTATG
CAAAAGGATATTCATGAGAAAGAATCAAAAACAATTGAAGATTTAGTCAGCAAAAATTTT
ATATTTTATACATATGAAAGTTTAAGTAGGCGAGTTCAAGGGCAGTCATTTGTTCATAAA
GTAAAAGTCATCAAAAATTCACAATTAGAAGAATATCGACATAAAACTCTTGATTCATCA
TTCAATGGTGTCGTATTTAACTATGAATATCAAGTCGTTTATCTTAACTTCCTTAACAAA
AAAGATTATTCTTATTTAATATTAAAAGAAAGATTTGTAACAAATCAAATGGTTTTTTAT
CTTCAAGAAAATCATTTTTTAAAAGATGCAATGAGTGAAAAGATTAATTGGTTTCGTGAT
TTTGGAATTCTTCATAAAATAATTTTAGAATATGTTGACAATTTTTTTCTTAATAAATTA
CCACCTGAAAAAGCAGCAAAATCATTAAAATTTCAAGAACTTTCTGCAATTTTTGGATTA
TGGCTAGCAGGACTAGGATTTTCTTTTATTGTGTGTCTTGTTGAAGTTGGAATTGGTTAT
AAAAAACCAATAAAAAATAGAAAGAAAACAAAAGTTGTAAAATTAATCAAAACTGATTCA
AATTTGCATGAATGA
>g988.t1 Gene=g988 Length=624
MRPFWIFFVLFILFSLVQGKIESLNNFQHPLSKATGDLIENVIKDSEIQNVRIIMLMSNE
SSLENVDIGNEIVKVATTKFKIQTRGNLRQPIDREKRISPVILMVDSIGTFNLSKLRIEH
DTPKFYLVILTKGIFKEIIEILDFFWKNSVSDVNFLVLNQTVVEMYTFFPFANKKCGTDL
SLVLINTFDLTTCTWSGNQFFPSKIKNLHKCQIKVGVSVNVPMVIFNNKTTQKYDGIEVT
LIREIAKEFDFVPQFTKPYESVGAINSNGSSSGLISEVYKRKLDVAIGSLSLQIDRTNYL
SATTSFATVPIVIVIPPTPQISPFAKLYLPFDFTTWSLLLAMFLIGYIVIIVTKLFAKTL
YKLIVGKNVNYPFTNMFIAFFGLSQNVLPKANFSRFLLAKFLIFCLVIRGLYQGKLFDIM
QKDIHEKESKTIEDLVSKNFIFYTYESLSRRVQGQSFVHKVKVIKNSQLEEYRHKTLDSS
FNGVVFNYEYQVVYLNFLNKKDYSYLILKERFVTNQMVFYLQENHFLKDAMSEKINWFRD
FGILHKIILEYVDNFFLNKLPPEKAAKSLKFQELSAIFGLWLAGLGFSFIVCLVEVGIGY
KKPIKNRKKTKVVKLIKTDSNLHE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g988.t1 | Gene3D | G3DSA:3.40.190.10 | - | 232 | 567 | 1.2E-35 |
| 11 | g988.t1 | Gene3D | G3DSA:3.40.190.10 | - | 310 | 517 | 1.2E-35 |
| 9 | g988.t1 | Gene3D | G3DSA:1.10.287.70 | - | 320 | 595 | 1.2E-35 |
| 2 | g988.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 80 | 598 | 1.3E-52 |
| 3 | g988.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 80 | 598 | 1.3E-52 |
| 1 | g988.t1 | Pfam | PF10613 | Ligated ion channel L-glutamate- and glycine-binding site | 220 | 315 | 1.3E-9 |
| 18 | g988.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 19 | g988.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 20 | g988.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 26 | g988.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 16 | g988.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 335 | - |
| 23 | g988.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 336 | 357 | - |
| 14 | g988.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 358 | 368 | - |
| 22 | g988.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 369 | 387 | - |
| 17 | g988.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 388 | 392 | - |
| 21 | g988.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 393 | 412 | - |
| 13 | g988.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 413 | 536 | - |
| 25 | g988.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 537 | 557 | - |
| 15 | g988.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 558 | 576 | - |
| 24 | g988.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 577 | 600 | - |
| 12 | g988.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 601 | 624 | - |
| 7 | g988.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 209 | 551 | 5.21E-21 |
| 8 | g988.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 4 | g988.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 334 | 356 | - |
| 6 | g988.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 369 | 388 | - |
| 5 | g988.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 577 | 599 | - |
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