General information for g5344.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Neuropeptide SIFamide receptor.
Parent gene
- The parent gene g5344 is located on chr_2: 9027527..9042441 (+ 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_2 | g5344 | g5344.t1 | TSS | g5344.t1 | 9026844 | 9026844 |
| chr_2 | g5344 | g5344.t1 | isoform | g5344.t1 | 9027527 | 9042441 |
| chr_2 | g5344 | g5344.t1 | exon | g5344.t1.exon1 | 9027527 | 9027676 |
| chr_2 | g5344 | g5344.t1 | cds | g5344.t1.CDS1 | 9027527 | 9027676 |
| chr_2 | g5344 | g5344.t1 | exon | g5344.t1.exon2 | 9028219 | 9028498 |
| chr_2 | g5344 | g5344.t1 | cds | g5344.t1.CDS2 | 9028219 | 9028498 |
| chr_2 | g5344 | g5344.t1 | exon | g5344.t1.exon3 | 9042338 | 9042441 |
| chr_2 | g5344 | g5344.t1 | cds | g5344.t1.CDS3 | 9042338 | 9042441 |
| chr_2 | g5344 | g5344.t1 | TTS | g5344.t1 | NA | NA |
Sequences
>g5344.t1 Gene=g5344 Length=534
ATGTTCAATTTATCAAATGACGAGATGGATTTTGCAACGTCTAGACCAGAAGAATATGAC
GAGATTGATAAATCATCGACCATTGAAGATTATTCTATAGAATATTCAAACAAATTAGCT
TCAAACAATATAACTCTCGATTTTGATCAGATCAGTGACGATTTACTAATCAATAACGAT
AACTATAATGACACTATACCGTACTTACAGTTAATGCGTCACTCATCGACAATATCCACA
ATATATATCATAGCTTACACGCTGGTATTTTCTGTTGGACTCGTCGGCAATTTGTTTGTC
ATTTCAGTTGTTTTTCGAGTGCCACGCATGAGATCTGTCACAAATTTATTCATCGCAAAT
TTAGCGTTTGCTGATGTGCTTGTGATTATCTTCTGTGTGCCTGCAACATTAATGAGCAAC
TTGTTTGTGCCATGGATTCTTGGTTGGTTTATGTGCAAAACAGTTCCTTATGTTCAAGGA
GTTTCAGTGGCTGCATCTGTTTATAGCTTAATTGCAGTATCTCTTGACAGGTGA
>g5344.t1 Gene=g5344 Length=177
MFNLSNDEMDFATSRPEEYDEIDKSSTIEDYSIEYSNKLASNNITLDFDQISDDLLINND
NYNDTIPYLQLMRHSSTISTIYIIAYTLVFSVGLVGNLFVISVVFRVPRMRSVTNLFIAN
LAFADVLVIIFCVPATLMSNLFVPWILGWFMCKTVPYVQGVSVAASVYSLIAVSLDR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5344.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 50 | 177 | 7.3E-34 |
| 2 | g5344.t1 | PANTHER | PTHR24241:SF168 | AGAP001379-PA | 56 | 177 | 1.3E-39 |
| 3 | g5344.t1 | PANTHER | PTHR24241 | NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR | 56 | 177 | 1.3E-39 |
| 6 | g5344.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 81 | 105 | 4.2E-18 |
| 7 | g5344.t1 | PRINTS | PR01012 | Neuropeptide Y receptor signature | 106 | 118 | 1.9E-6 |
| 5 | g5344.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 114 | 135 | 4.2E-18 |
| 9 | g5344.t1 | PRINTS | PR01012 | Neuropeptide Y receptor signature | 136 | 148 | 1.9E-6 |
| 4 | g5344.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 159 | 177 | 4.2E-18 |
| 8 | g5344.t1 | PRINTS | PR01012 | Neuropeptide Y receptor signature | 159 | 174 | 1.9E-6 |
| 1 | g5344.t1 | Pfam | PF00001 | 7 transmembrane receptor (rhodopsin family) | 96 | 177 | 7.4E-19 |
| 14 | g5344.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 80 | - |
| 16 | g5344.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 105 | - |
| 13 | g5344.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 106 | 116 | - |
| 18 | g5344.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 117 | 137 | - |
| 15 | g5344.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 138 | 156 | - |
| 17 | g5344.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 157 | 175 | - |
| 12 | g5344.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 176 | 177 | - |
| 22 | g5344.t1 | ProSiteProfiles | PS50262 | G-protein coupled receptors family 1 profile. | 96 | 177 | 21.395 |
| 10 | g5344.t1 | SUPERFAMILY | SSF81321 | Family A G protein-coupled receptor-like | 61 | 177 | 1.01E-27 |
| 19 | g5344.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 81 | 103 | - |
| 20 | g5344.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 138 | - |
| 21 | g5344.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 175 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5344/g5344.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5344.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0007186 | G protein-coupled receptor signaling pathway | BP |
| GO:0004983 | neuropeptide Y receptor activity | MF |
| GO:0016021 | integral component of membrane | CC |
| GO:0004930 | G protein-coupled 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