General information for g13890.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cholecystokinin receptor.
Parent gene
- The parent gene g13890 is located on chr_1: 33142665..33151238 (- 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_1 | g13890 | g13890.t1 | isoform | g13890.t1 | 33142665 | 33151238 |
| chr_1 | g13890 | g13890.t1 | exon | g13890.t1.exon1 | 33142665 | 33143184 |
| chr_1 | g13890 | g13890.t1 | cds | g13890.t1.CDS1 | 33142665 | 33143184 |
| chr_1 | g13890 | g13890.t1 | exon | g13890.t1.exon2 | 33144411 | 33144546 |
| chr_1 | g13890 | g13890.t1 | cds | g13890.t1.CDS2 | 33144411 | 33144546 |
| chr_1 | g13890 | g13890.t1 | exon | g13890.t1.exon3 | 33144673 | 33144858 |
| chr_1 | g13890 | g13890.t1 | cds | g13890.t1.CDS3 | 33144673 | 33144858 |
| chr_1 | g13890 | g13890.t1 | exon | g13890.t1.exon4 | 33144942 | 33145139 |
| chr_1 | g13890 | g13890.t1 | cds | g13890.t1.CDS4 | 33144942 | 33145139 |
| chr_1 | g13890 | g13890.t1 | exon | g13890.t1.exon5 | 33151178 | 33151238 |
| chr_1 | g13890 | g13890.t1 | cds | g13890.t1.CDS5 | 33151178 | 33151238 |
| chr_1 | g13890 | g13890.t1 | TSS | g13890.t1 | NA | NA |
| chr_1 | g13890 | g13890.t1 | TTS | g13890.t1 | NA | NA |
Sequences
>g13890.t1 Gene=g13890 Length=1101
ATGTTGTTACGTGATTTCATTTTTGGTGAAATTATGTGCAAGCTGCTTCCATATTTGCAA
GCAACATCGGTAAGCGTTTCGGCATGGACGCTCGTAGCAATAAGTGTTGAAAGATATTGT
GCGATTTGTCATCCCTTAAGATCACGACGATGGCAAACGCTCAATCATGCCTACAAGTCG
ATTGTTTTAATTTGGATAGCGAGCTTATTTTTCATGCTGCCAATTGCCGCCCTCAGTAAA
CTTATACCAACGAGTCAGGGTCATAAAAAATGTCGCGAAGTTTGGCCCAACGAGCCAGTT
CATTATGAACAACTGTACAACTTGTTTTTGGATATACTCTTGTTAGTGCTTCCTCTTGTA
GTACTAGCTGCTGCTTATACGATGATATCTCGTACCCTATGGCAGAGTATAGATGCGGAA
AAAGAGATCGTTAAACAGGCATCAGTATATTCCAACGCCTCATCATCACGTAAGCGACAA
AAAGTGAATGATGGCATCTCATTCCAAAAACTTCGCAACTCATCACAAGAAATAATGTTG
TTAAATCGTGATTCCAAGAAACATACATTCGGCCTAAGGAGATCTAATCCAGCAAAAAGT
TTACTCAACAAGCGTCGTGTTATCAAAATGTTATTTGTCGTTGTCATTGAATTCTTCATT
TGTTGGACGCCACTCTATATAATAAATACAATTGCCCTTTTTGATCCAAAGGCTGTCTAT
CAGCATCTTGGTTACACTGCTATAAGTTTTTTTCAACTACTAGCATATTCATCCTCCTGC
TGTAATCCAATAACGTACTGTTTCATGTCCATGGGATTTCGAAAAGCATTTATGAACTTA
TTTCGGTGTTTTCGCCATGAGCCCGGCAGACGGATCAGTGTCAGTGGATATTGTATAAAT
ACATCAGCCGGAAGCGCTGAAGCGTGCCAAATACTGGCAGCAACCGTCAATTCTATCATG
CAGAACGAAAGCAGCAATAGCATACCTGAAAACGAAAATGAACATGATATAGATCTTAAA
AATAGTTTCAACTTTCAGGAGCTCACATTCAATGACTATCTGAATCAGGAAGGAAAAGTT
TCTACAGATTTTATAGATTAA
>g13890.t1 Gene=g13890 Length=366
MLLRDFIFGEIMCKLLPYLQATSVSVSAWTLVAISVERYCAICHPLRSRRWQTLNHAYKS
IVLIWIASLFFMLPIAALSKLIPTSQGHKKCREVWPNEPVHYEQLYNLFLDILLLVLPLV
VLAAAYTMISRTLWQSIDAEKEIVKQASVYSNASSSRKRQKVNDGISFQKLRNSSQEIML
LNRDSKKHTFGLRRSNPAKSLLNKRRVIKMLFVVVIEFFICWTPLYIINTIALFDPKAVY
QHLGYTAISFFQLLAYSSSCCNPITYCFMSMGFRKAFMNLFRCFRHEPGRRISVSGYCIN
TSAGSAEACQILAATVNSIMQNESSNSIPENENEHDIDLKNSFNFQELTFNDYLNQEGKV
STDFID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g13890.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 1 | 164 | 3.2E-39 |
| 17 | g13890.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 166 | 321 | 7.0E-28 |
| 3 | g13890.t1 | PANTHER | PTHR24238 | G-PROTEIN COUPLED RECEPTOR | 2 | 151 | 4.0E-96 |
| 5 | g13890.t1 | PANTHER | PTHR24238:SF46 | TYRAMINE/OCTOPAMINE RECEPTOR-LIKE PROTEIN | 2 | 151 | 4.0E-96 |
| 2 | g13890.t1 | PANTHER | PTHR24238 | G-PROTEIN COUPLED RECEPTOR | 192 | 345 | 4.0E-96 |
| 4 | g13890.t1 | PANTHER | PTHR24238:SF46 | TYRAMINE/OCTOPAMINE RECEPTOR-LIKE PROTEIN | 192 | 345 | 4.0E-96 |
| 10 | g13890.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 20 | 42 | 1.7E-27 |
| 8 | g13890.t1 | PRINTS | PR01822 | Cholecystokinin receptor family signature | 43 | 57 | 5.3E-10 |
| 14 | g13890.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 56 | 77 | 1.7E-27 |
| 13 | g13890.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 107 | 130 | 1.7E-27 |
| 7 | g13890.t1 | PRINTS | PR01822 | Cholecystokinin receptor family signature | 126 | 140 | 5.3E-10 |
| 6 | g13890.t1 | PRINTS | PR01822 | Cholecystokinin receptor family signature | 199 | 210 | 5.3E-10 |
| 12 | g13890.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 207 | 231 | 1.7E-27 |
| 9 | g13890.t1 | PRINTS | PR01822 | Cholecystokinin receptor family signature | 233 | 250 | 5.3E-10 |
| 11 | g13890.t1 | PRINTS | PR00237 | Rhodopsin-like GPCR superfamily signature | 248 | 274 | 1.7E-27 |
| 1 | g13890.t1 | Pfam | PF00001 | 7 transmembrane receptor (rhodopsin family) | 4 | 266 | 1.4E-45 |
| 22 | g13890.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 14 | - |
| 28 | g13890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 36 | - |
| 20 | g13890.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 37 | 56 | - |
| 27 | g13890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 57 | 77 | - |
| 21 | g13890.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 78 | 104 | - |
| 26 | g13890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 105 | 126 | - |
| 19 | g13890.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 127 | 206 | - |
| 25 | g13890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 207 | 228 | - |
| 23 | g13890.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 229 | 247 | - |
| 24 | g13890.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 248 | 269 | - |
| 18 | g13890.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 270 | 366 | - |
| 34 | g13890.t1 | ProSitePatterns | PS00237 | G-protein coupled receptors family 1 signature. | 26 | 42 | - |
| 35 | g13890.t1 | ProSiteProfiles | PS50262 | G-protein coupled receptors family 1 profile. | 1 | 266 | 35.096 |
| 15 | g13890.t1 | SUPERFAMILY | SSF81321 | Family A G protein-coupled receptor-like | 2 | 292 | 1.74E-55 |
| 29 | g13890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
| 33 | g13890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 57 | 79 | - |
| 32 | g13890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 108 | 130 | - |
| 30 | g13890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 211 | 233 | - |
| 31 | g13890.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 248 | 270 | - |
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: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 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