General information for g5346.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Neuropeptide SIFamide receptor.
Parent gene
- The parent gene g5346 is located on chr_2: 9054651..9060726 (+ 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 | g5346 | g5346.t1 | isoform | g5346.t1 | 9054651 | 9060726 |
| chr_2 | g5346 | g5346.t1 | exon | g5346.t1.exon1 | 9054651 | 9054703 |
| chr_2 | g5346 | g5346.t1 | cds | g5346.t1.CDS1 | 9054651 | 9054703 |
| chr_2 | g5346 | g5346.t1 | exon | g5346.t1.exon2 | 9058630 | 9058912 |
| chr_2 | g5346 | g5346.t1 | cds | g5346.t1.CDS2 | 9058630 | 9058912 |
| chr_2 | g5346 | g5346.t1 | exon | g5346.t1.exon3 | 9059033 | 9059186 |
| chr_2 | g5346 | g5346.t1 | cds | g5346.t1.CDS3 | 9059033 | 9059186 |
| chr_2 | g5346 | g5346.t1 | exon | g5346.t1.exon4 | 9059272 | 9059440 |
| chr_2 | g5346 | g5346.t1 | cds | g5346.t1.CDS4 | 9059272 | 9059440 |
| chr_2 | g5346 | g5346.t1 | exon | g5346.t1.exon5 | 9059576 | 9060315 |
| chr_2 | g5346 | g5346.t1 | cds | g5346.t1.CDS5 | 9059576 | 9060315 |
| chr_2 | g5346 | g5346.t1 | exon | g5346.t1.exon6 | 9060644 | 9060726 |
| chr_2 | g5346 | g5346.t1 | cds | g5346.t1.CDS6 | 9060644 | 9060726 |
| chr_2 | g5346 | g5346.t1 | TSS | g5346.t1 | NA | NA |
| chr_2 | g5346 | g5346.t1 | TTS | g5346.t1 | NA | NA |
Sequences
>g5346.t1 Gene=g5346 Length=1482
ATGCTTATTTTTGGTTTTGTCCGTATACTTTTGGCCGCTACTGTACCTAAAAAATTACTT
GCTATATGGTGGCCTTTAAAATTACAAATCTCAAAAAAGCGGGCGAAAGGGATTATCATC
GGAATTTGGGTCATCGCATTGTCTATAACCCTTCCGTGGGCATTGTTCTTTCAACTTGTT
CCATTCGATATATCAAGGCCCGATATTGAGTTATGCTTAGAAATATGGCCAGATGGCAGC
GATGGTACGCTTTACTTTCTATTTGCCAACCTACTCGCCTGTTATGTGATTCCAATGGCA
TTGATATCAATTTGCTATATTTTGATATGGATAAAGGTGGCAACCAGAGACATACCCGGT
GATACAAAAGAAAAGGATCGTATTCAACAACAGTCGAAAATCAAAGTTGTTAAAATGCTG
GCACTTGTGGTCATATTGTTTGTACTCTCATGGCTTCCACTTTATGCAATTTTCACCATC
AAAAAGTTTGGTTCACCTGATCCGAAAATGGAAGAGAATCTCAATATTTTAGCACCAATT
GCTCAATGGTTAGGATCTGCGAACAGCTGCCTAAATCCTATATTGTATGCATTCAATGAG
AAATATCGACGTGGTTTCATTGCCATAATCCGTTCACGTAAATGCTGGGGCCGATTGAGA
TACTATGAAACAGTTGCAATAACATCGTCATCAGCAAGTACAAGAAAATCTTCACACTAT
AACAATTACAATAGTACACGAAAGGCACCATATAGTCCATCCATGAAGTCTGATGCTGTT
TCTTTCATATATGATCAGAATAATATGAATGGCAATAGTAACAATGCCAATAGTAGAACC
AAACACAATGGTTTATCAAAGCAAAATAGCAATTTGTCACGACAAATGCTGCTCAAGCAA
GACTCGAGTGTTTCAAGAAATTCATTTATGAAGCAAGATAGTGTGCAGTCAACACGACAA
ATATTGGCGAACAATCAGAACAAATCTGAACATATGACCGAATACTTGTGTCGACAAGAT
AGCGGTAATTCGTGCAAAGCCTTACTGAAACAAGACAGCAATGGCTCAATATTGTCAAAG
CAAAATTCTCAGGTGTCTTATAGTGAATCGAAAAGGAGCTTTTCATCGTCCATTGACTCA
TGTACGGATTTAAGGAAGGAGTCAATTTTGAGGCAAAACTTTCAAAACGCTTATTTGGAA
CAAAAGAAAAAAACTTTATCAAAACAAGACACAGAAATATCACTAATAGAAGAGAATCGA
AGTGGTAGTGGTATTGGTAATTCATTGATTAATAGTCAAGACAGTTGTGCTTCATTGATT
TCTACTAGCTCTGCTATGAGACGACAACGGTTGGTGAAACAAGATTCTATCTTCTCCTTC
GGTGAGCCCATTCGAAGTGTTGCTGATGGCAAACGACGAGATTTTATCAAACAGGATTCT
ATGGTTTCCGTTTCCTTTGCTGACCATCATGAAATCATTTAA
>g5346.t1 Gene=g5346 Length=493
MLIFGFVRILLAATVPKKLLAIWWPLKLQISKKRAKGIIIGIWVIALSITLPWALFFQLV
PFDISRPDIELCLEIWPDGSDGTLYFLFANLLACYVIPMALISICYILIWIKVATRDIPG
DTKEKDRIQQQSKIKVVKMLALVVILFVLSWLPLYAIFTIKKFGSPDPKMEENLNILAPI
AQWLGSANSCLNPILYAFNEKYRRGFIAIIRSRKCWGRLRYYETVAITSSSASTRKSSHY
NNYNSTRKAPYSPSMKSDAVSFIYDQNNMNGNSNNANSRTKHNGLSKQNSNLSRQMLLKQ
DSSVSRNSFMKQDSVQSTRQILANNQNKSEHMTEYLCRQDSGNSCKALLKQDSNGSILSK
QNSQVSYSESKRSFSSSIDSCTDLRKESILRQNFQNAYLEQKKKTLSKQDTEISLIEENR
SGSGIGNSLINSQDSCASLISTSSAMRRQRLVKQDSIFSFGEPIRSVADGKRRDFIKQDS
MVSVSFADHHEII
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5346.t1 | Coils | Coil | Coil | 399 | 419 | - |
| 9 | g5346.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 5 | 252 | 2.6E-50 |
| 2 | g5346.t1 | PANTHER | PTHR24241:SF148 | NEUROPEPTIDE SIFAMIDE RECEPTOR | 10 | 262 | 7.7E-87 |
| 3 | g5346.t1 | PANTHER | PTHR24241 | NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR | 10 | 262 | 7.7E-87 |
| 7 | g5346.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 34 | 55 | 7.5E-19 |
| 4 | g5346.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 87 | 110 | 7.5E-19 |
| 6 | g5346.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 136 | 160 | 7.5E-19 |
| 5 | g5346.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 178 | 204 | 7.5E-19 |
| 1 | g5346.t1 | Pfam | PF00001 | 7 transmembrane receptor (rhodopsin family) | 20 | 196 | 4.9E-27 |
| 15 | g5346.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 19 | g5346.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 26 | - |
| 12 | g5346.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 27 | 37 | - |
| 18 | g5346.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 38 | 62 | - |
| 16 | g5346.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 63 | 81 | - |
| 21 | g5346.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 115 | - |
| 11 | g5346.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 116 | 135 | - |
| 20 | g5346.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 160 | - |
| 14 | g5346.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 161 | 179 | - |
| 17 | g5346.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 180 | 198 | - |
| 13 | g5346.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 199 | 493 | - |
| 26 | g5346.t1 | ProSiteProfiles | PS50262 | G-protein coupled receptors family 1 profile. | 1 | 196 | 25.989 |
| 8 | g5346.t1 | SUPERFAMILY | SSF81321 | Family A G protein-coupled receptor-like | 19 | 218 | 5.4E-34 |
| 22 | g5346.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
| 24 | g5346.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 38 | 60 | - |
| 25 | g5346.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 86 | 108 | - |
| 23 | g5346.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 136 | 158 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5346/g5346.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5346.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 K08375 (neuropeptide FF 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