General information for g2556.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Calcitonin gene-related peptide type 1 receptor.
Parent gene
- The parent gene g2556 is located on chr_3: 18663390..18669677 (- 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 | g2556 | g2556.t1 | TTS | g2556.t1 | 18662497 | 18662497 |
| chr_3 | g2556 | g2556.t1 | isoform | g2556.t1 | 18663390 | 18669677 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon1 | 18663390 | 18663766 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS1 | 18663390 | 18663766 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon2 | 18663830 | 18663903 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS2 | 18663830 | 18663903 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon3 | 18665015 | 18665362 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS3 | 18665015 | 18665362 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon4 | 18665430 | 18665521 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS4 | 18665430 | 18665521 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon5 | 18665592 | 18665782 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS5 | 18665592 | 18665782 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon6 | 18665846 | 18665890 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS6 | 18665846 | 18665890 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon7 | 18665951 | 18666052 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS7 | 18665951 | 18666052 |
| chr_3 | g2556 | g2556.t1 | exon | g2556.t1.exon8 | 18669671 | 18669677 |
| chr_3 | g2556 | g2556.t1 | cds | g2556.t1.CDS8 | 18669671 | 18669677 |
| chr_3 | g2556 | g2556.t1 | TSS | g2556.t1 | 18669810 | 18669810 |
Sequences
>g2556.t1 Gene=g2556 Length=1236
ATGGAAGATAACATAACGAGCAGCACACCGGAAGGTGGAATTTTATTGATAAAGAAACTG
TACAAACAATGCTTGCAATTAGCCTGGCAGTTAAATAACAGTAGTGCTGTAAATAACACA
GATTCGCCACCACAATGTCCAGTAATATTTGATGGTTTCACTTGTTGGGGGCCAACAAAA
ATTAATACAACTGATTATAAACCATGTCCATCATATGTAATTGGATTCAATGGAAATTCA
AATGCTTCAAAAGTCTGCTTAGAAAATGGATCATGGTATACAAATCCAAATACAGGACAA
CATTGGACAAATTATTTAGCTTGTGTTGACCATGAGGACTATACTTTCCGACAAACAATT
AACGATATTTATTTCTACGGTTATTGCGTTTCACTCTCAACACTCATAATTTCATTAGTC
ATATTTCTCAGCTTTAGATCATTAAAATGTACAAGAATTAAAATACATGTGCAATTATTC
ATCTCTTTGGCAATGAGTTGCATTTTATGGATAATCTGGTATAAATTTATCATTATTGAT
CCAAACATCGTGAAGGAAAATTCTTTAGGATGCATTGGCTTGCATATTGTACTGCAATAT
TTGATGATATGCAATTATTTCTGGATGTTCTGTGAGGGACTTCATTTGCATCTTGTGTTG
GTTGTTGTCTTTATAAAAGATAATGTTGCCATGCGAATATTCTTCATTATTGGATGGCTT
TTGCCTTTACTTATCATCACTGCATACAGCTTAATGAGGATGTATAATACAGTTGATAAT
AACTTATGTTGGATCGAGGAGAGTCATTATCAATATATTCTCACAATTCCTGTCTTAATC
TCCTTCATTTGCTCAATTATCTTCTTAGTGAACATAGTTCGAGTTCTAATTACAAAACTA
CATCCGAAATCAGAAGCACCGCCACCATTAGCAATAAAAAAGGCAGTTCGTGCGACATTA
ATTCTCATTCCATTGTTTGGATTACAGCATGTTCTCATTCCATTCAGACCAGAAAAAGGA
TCATCATTTGAAAGTATTTATCAAATTGTGTCTGCCGTTTTTGTAAGCCTTCAAGGACTT
TGTGTGTCATGTCTATTCTGCTTCGCTAATCACGAAGTTATTTCTGCCGTGTTTAGCTAT
TTGAGTAGTATATTTCCCATGATTTTCAAGACATCTTCGCGTGAAAATTATAACAATCTA
GGACAACCAACGACGACGAGAGATATTGTATTATAA
>g2556.t1 Gene=g2556 Length=411
MEDNITSSTPEGGILLIKKLYKQCLQLAWQLNNSSAVNNTDSPPQCPVIFDGFTCWGPTK
INTTDYKPCPSYVIGFNGNSNASKVCLENGSWYTNPNTGQHWTNYLACVDHEDYTFRQTI
NDIYFYGYCVSLSTLIISLVIFLSFRSLKCTRIKIHVQLFISLAMSCILWIIWYKFIIID
PNIVKENSLGCIGLHIVLQYLMICNYFWMFCEGLHLHLVLVVVFIKDNVAMRIFFIIGWL
LPLLIITAYSLMRMYNTVDNNLCWIEESHYQYILTIPVLISFICSIIFLVNIVRVLITKL
HPKSEAPPPLAIKKAVRATLILIPLFGLQHVLIPFRPEKGSSFESIYQIVSAVFVSLQGL
CVSCLFCFANHEVISAVFSYLSSIFPMIFKTSSRENYNNLGQPTTTRDIVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 32 | g2556.t1 | CDD | cd15260 | 7tmB1_NPR_B4_insect-like | 117 | 382 | 1.05333E-130 |
| 14 | g2556.t1 | Gene3D | G3DSA:4.10.1240.10 | Hormone receptor superfamily | 11 | 110 | 4.5E-23 |
| 13 | g2556.t1 | Gene3D | G3DSA:1.20.1070.10 | - | 111 | 395 | 3.6E-66 |
| 3 | g2556.t1 | PANTHER | PTHR45620 | PDF RECEPTOR-LIKE PROTEIN-RELATED | 35 | 400 | 6.4E-123 |
| 4 | g2556.t1 | PANTHER | PTHR45620:SF31 | HECTOR, ISOFORM A | 35 | 400 | 6.4E-123 |
| 7 | g2556.t1 | PRINTS | PR00249 | Secretin-like GPCR superfamily signature | 122 | 146 | 2.8E-46 |
| 5 | g2556.t1 | PRINTS | PR00249 | Secretin-like GPCR superfamily signature | 154 | 178 | 2.8E-46 |
| 11 | g2556.t1 | PRINTS | PR00249 | Secretin-like GPCR superfamily signature | 193 | 216 | 2.8E-46 |
| 6 | g2556.t1 | PRINTS | PR00249 | Secretin-like GPCR superfamily signature | 231 | 256 | 2.8E-46 |
| 8 | g2556.t1 | PRINTS | PR00249 | Secretin-like GPCR superfamily signature | 272 | 297 | 2.8E-46 |
| 10 | g2556.t1 | PRINTS | PR00249 | Secretin-like GPCR superfamily signature | 315 | 335 | 2.8E-46 |
| 9 | g2556.t1 | PRINTS | PR00249 | Secretin-like GPCR superfamily signature | 348 | 369 | 2.8E-46 |
| 1 | g2556.t1 | Pfam | PF02793 | Hormone receptor domain | 44 | 110 | 1.2E-12 |
| 2 | g2556.t1 | Pfam | PF00002 | 7 transmembrane receptor (Secretin family) | 122 | 362 | 8.8E-55 |
| 22 | g2556.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 122 | - |
| 27 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 123 | 145 | - |
| 15 | g2556.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 146 | 156 | - |
| 26 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 157 | 177 | - |
| 19 | g2556.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 178 | 196 | - |
| 28 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 197 | 225 | - |
| 17 | g2556.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 226 | 231 | - |
| 30 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 252 | - |
| 20 | g2556.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 253 | 271 | - |
| 29 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 272 | 294 | - |
| 16 | g2556.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 295 | 314 | - |
| 31 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 315 | 333 | - |
| 23 | g2556.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 334 | 344 | - |
| 25 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 345 | 366 | - |
| 18 | g2556.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 367 | 372 | - |
| 24 | g2556.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 373 | 389 | - |
| 21 | g2556.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 390 | 411 | - |
| 40 | g2556.t1 | ProSitePatterns | PS00649 | G-protein coupled receptors family 2 signature 1. | 46 | 70 | - |
| 42 | g2556.t1 | ProSiteProfiles | PS50227 | G-protein coupled receptors family 2 profile 1. | 23 | 112 | 17.458 |
| 41 | g2556.t1 | ProSiteProfiles | PS50261 | G-protein coupled receptors family 2 profile 2. | 120 | 370 | 34.903 |
| 39 | g2556.t1 | SMART | SM00008 | HormR_1 | 42 | 117 | 2.0E-10 |
| 12 | g2556.t1 | SUPERFAMILY | SSF111418 | Hormone receptor domain | 17 | 115 | 6.15E-22 |
| 33 | g2556.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 123 | 145 | - |
| 38 | g2556.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 155 | 174 | - |
| 37 | g2556.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 187 | 209 | - |
| 34 | g2556.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 229 | 251 | - |
| 36 | g2556.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 272 | 294 | - |
| 35 | g2556.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 346 | 368 | - |
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:0007186 | G protein-coupled receptor signaling pathway | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0004888 | transmembrane signaling receptor activity | MF |
| GO:0007166 | cell surface receptor signaling pathway | BP |
| 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