General information for g5827.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Somatostatin receptor type 2.
Parent gene
- The parent gene g5827 is located on chr_2: 12090565..12093721 (- 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 | g5827 | g5827.t1 | isoform | g5827.t1 | 12090565 | 12093721 |
| chr_2 | g5827 | g5827.t1 | exon | g5827.t1.exon1 | 12090565 | 12090717 |
| chr_2 | g5827 | g5827.t1 | cds | g5827.t1.CDS1 | 12090565 | 12090717 |
| chr_2 | g5827 | g5827.t1 | exon | g5827.t1.exon2 | 12091123 | 12091418 |
| chr_2 | g5827 | g5827.t1 | cds | g5827.t1.CDS2 | 12091123 | 12091418 |
| chr_2 | g5827 | g5827.t1 | exon | g5827.t1.exon3 | 12093124 | 12093721 |
| chr_2 | g5827 | g5827.t1 | cds | g5827.t1.CDS3 | 12093124 | 12093721 |
| chr_2 | g5827 | g5827.t1 | TSS | g5827.t1 | NA | NA |
| chr_2 | g5827 | g5827.t1 | TTS | g5827.t1 | NA | NA |
Sequences
>g5827.t1 Gene=g5827 Length=1047
ATGCAAAACTTGAGTGGGTCAATGAACAGTTCGACGCGTTTCTTTCGACCGCACATCAAT
GACACAAGAATGAATTTTCAATTTTGGTTGCATTCTTTCTACAACTATCCTTTCGCTCTC
AATTTCACTTCAAACGATTCATCGCCCTATTTAAATTGCGCCTCAACTCAAAATCCTACG
GGAAATGTGATAGCCATGATACTTTACATCATCGTATGCTGTGTAGGTCTCTTCGGCAAC
ACCCTCGTTATTTATGTTGTTCTGAAATTCTCAAAAATGCAAACTGTAACAAATAGATAT
ATATTGAACTTGGCAATTGCCGATGAATGCTTTCTCATAGGCATTCCATTTCTATTAACA
ACAATGTATCTTAATGAATGGATTTTTGGATCTTTCCTTTGCAAACTTTATATGGTATCG
ACCTCAATCACGCAATTTTCTTCTTCCATATTCTTGTTAATTATGTCAGCAGATAGATTT
ATTGCAGTTTGCCATCCTATCTCATCGCCTCGATTTCGAACGCAATTAGTTTCGAAAATT
GTGTCATTATTGGCGTGGGGACTCAGCATCATCATTATGCTTCCTGTTATGTTGTATGCA
AATACAACCGAAAAGTTCCCGGGCTCAGAACAAATGACGTGCAATATTTTATGGTCACAC
CCAAGCAACATTGACGGCCAACTAGGCGGTTCAACGTTTACATTGTATTCGCTAATCTTA
GGATTTGCCGTTCCATTAAGTCTCATCCTCGTTTTCTATTATTTAGTCATTAAGAAGTTG
CAGACTGTTGGGCCGAAAAATAAGTCCAAGGATAAAAAACGATCACATCGCAAAGTGACT
AGGCTTGTTCTTACCGTTATTACAGTTTATATCCTCTGCTGGTCGCCGTATTGGGTTAGT
CAAATGGCACTTATAAATTCGCCGCCAGATGTTTGTCAAACTAAATTGGAAATAACGGTT
TTTGTTTTGGTCGGAGCATTAGGATACAGTAACTCCTCTATCAATCCTATCTTGTATGCG
TTCTTAAGGTACGTTTTGTTTATTTAA
>g5827.t1 Gene=g5827 Length=348
MQNLSGSMNSSTRFFRPHINDTRMNFQFWLHSFYNYPFALNFTSNDSSPYLNCASTQNPT
GNVIAMILYIIVCCVGLFGNTLVIYVVLKFSKMQTVTNRYILNLAIADECFLIGIPFLLT
TMYLNEWIFGSFLCKLYMVSTSITQFSSSIFLLIMSADRFIAVCHPISSPRFRTQLVSKI
VSLLAWGLSIIIMLPVMLYANTTEKFPGSEQMTCNILWSHPSNIDGQLGGSTFTLYSLIL
GFAVPLSLILVFYYLVIKKLQTVGPKNKSKDKKRSHRKVTRLVLTVITVYILCWSPYWVS
QMALINSPPDVCQTKLEITVFVLVGALGYSNSSINPILYAFLRYVLFI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5827.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 50 | 344 | 2.4E-77 |
| 2 | g5827.t1 | PANTHER | PTHR24229:SF51 | ALLATOSTATIN C RECEPTOR 1-RELATED | 53 | 342 | 4.3E-118 |
| 3 | g5827.t1 | PANTHER | PTHR24229 | NEUROPEPTIDES RECEPTOR | 53 | 342 | 4.3E-118 |
| 10 | g5827.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 64 | 88 | 1.1E-42 |
| 7 | g5827.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 97 | 118 | 1.1E-42 |
| 4 | g5827.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 141 | 163 | 1.1E-42 |
| 6 | g5827.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 177 | 198 | 1.1E-42 |
| 5 | g5827.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 234 | 257 | 1.1E-42 |
| 9 | g5827.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 279 | 303 | 1.1E-42 |
| 8 | g5827.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 321 | 347 | 1.1E-42 |
| 1 | g5827.t1 | Pfam | PF00001 | 7 transmembrane receptor (rhodopsin family) | 79 | 339 | 2.8E-55 |
| 18 | g5827.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 65 | - |
| 21 | g5827.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 88 | - |
| 13 | g5827.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 89 | 99 | - |
| 27 | g5827.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 100 | 124 | - |
| 17 | g5827.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 125 | 135 | - |
| 26 | g5827.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 155 | - |
| 15 | g5827.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 156 | 175 | - |
| 25 | g5827.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 200 | - |
| 19 | g5827.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 201 | 234 | - |
| 23 | g5827.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 257 | - |
| 16 | g5827.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 258 | 277 | - |
| 22 | g5827.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 278 | 298 | - |
| 20 | g5827.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 299 | 317 | - |
| 24 | g5827.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 318 | 342 | - |
| 14 | g5827.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 343 | 348 | - |
| 35 | g5827.t1 | ProSitePatterns | PS00237 | G-protein coupled receptors family 1 signature. | 147 | 163 | - |
| 37 | g5827.t1 | ProSiteProfiles | PS50262 | G-protein coupled receptors family 1 profile. | 79 | 339 | 44.865 |
| 36 | g5827.t1 | SMART | SM01381 | 7TM_GPCR_Srsx_2 | 73 | 346 | 4.2E-4 |
| 11 | g5827.t1 | SUPERFAMILY | SSF81321 | Family A G protein-coupled receptor-like | 34 | 342 | 2.93E-60 |
| 29 | g5827.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 88 | - |
| 28 | g5827.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 100 | 122 | - |
| 33 | g5827.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 137 | 156 | - |
| 32 | g5827.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 198 | - |
| 30 | g5827.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 235 | 257 | - |
| 31 | g5827.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 278 | 300 | - |
| 34 | g5827.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 320 | 342 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5827/g5827.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5827.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0007186 | G protein-coupled receptor signaling pathway | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0004930 | G protein-coupled receptor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K04218 (somatostatin receptor 2)
Pathway
- This transcript belongs to the following pathways
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