RetrogeneDB ID: | retro_cjac_2708 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:28249059..28249885(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GPR180 | ||
| Ensembl ID: | ENSCJAG00000003277 | ||
| Aliases: | None | ||
| Description: | G protein-coupled receptor 180 [Source:HGNC Symbol;Acc:28899] |
Retrocopy-Parental alignment summary:
>retro_cjac_2708
CTGTGGCTACTGGTGGTGGCCCTCACATGCTGCTGGTGGCCACAGAGCAGCCAAAGTAAGACCCTTTTTGGCAGCTTCAG
CAACACCGCAGCCCAAGATGCTGAGGGCCAGCACATCTGCCGCTTCAAGTTCCATGGTGACCATGCTCTTCTGTGTGTCA
GAATCAACAACACAGACATAGCTGTTGAAAAACAAGCTAAACCCTACCTGTTCCAAGCTCAGGAATGGATAAAGCTACAG
AAAAGCAGTCATGGTTATAGCTGCAGTAAAAAATTATCCAAAGTTTAGTTGACAATGACAATGAACCAGACTAAACATAA
TCTGACAGTGTCCCAGATTCCATCTCTGCAAACATGGCATGGGTTTTATGTAGACAAGTATACGTGCCAAGATGACAAGG
ACACTCAGGTGGACAATACCCATTTGAAATGGTGTTACTAAACCCAGATGCTAAAGGGAATTCATTTGATCATTTTACTG
CTGGAGAATCAGGGTTGCCTGAATTCTTTTTCCTCCTAGTCCTAGTGTACTTTGTGATTGCTTGCATTTATGCTCAATCA
TTGTGACAGGCTATTAAGAAAGGAAGACCCATGCACATGATTTTAAAGGTTCTGCCAACTGCATTGCTCTTATGGCTGGT
TCAGCTTTAGCTAATTACATTTATTTCTCCAGCTACTCCAAAGATGGAATAGGGGTACCATTTATGTGAAGTTCTGCAGA
ATTTTTTGACACCACTTTCCAAATTCAGATGTCATACCTACTTTTGAGTCTATGCATGGGTTGGACAATAGTCAGAATGA
AGAAGTCTCAAAGCAGACCTCTCCAG
ORF - retro_cjac_2708 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.72 % |
| Parental protein coverage: | 62.95 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LRLLAVALTCCWWPQGSQGKTLRGSFSSTVAQDAQGQRIGHFEFHGDHALLCVRINNIAVAVGKEAKLYL |
| L.LL.VALTCCWWPQ.SQ.KTL.GSFS.T.AQDA.GQ.I..F.FHGDHALLCVRINN...AV.K.AK.YL | |
| Retrocopy | LWLLVVALTCCWWPQSSQSKTLFGSFSNTAAQDAEGQHICRFKFHGDHALLCVRINNTDIAVEKQAKPYL |
| Parental | FQAQEWLKLQESSHGYSCSEKLSKAQLTMTMNQTEHNLTVSQIPSPQTWHVFYADKYTCQDDKENSQVED |
| FQAQEW.KLQ.SSHGYSCS.KLSK..LTMTMNQT.HNLTVSQIPS.QTWH.FY.DKYTCQDDK...QV.. | |
| Retrocopy | FQAQEWIKLQKSSHGYSCSKKLSKV*LTMTMNQTKHNLTVSQIPSLQTWHGFYVDKYTCQDDKD-TQVDN |
| Parental | -IPFEMVLLNPDAEGNPFDHFSAGESGLHEFFFLLVLVYFVIACIYAQSLWQAIKKGGPMHMILKVLTTA |
| ..PFEMVLLNPDA.GN.FDHF.AGESGL.EFFFLLVLVYFVIACIYAQSL.QAIKKG.PMHMILKVL.TA | |
| Retrocopy | <YPFEMVLLNPDAKGNSFDHFTAGESGLPEFFFLLVLVYFVIACIYAQSL*QAIKKGRPMHMILKVLPTA |
| Parental | LL-LQAGSALANYIHFSSYSRDGIGVPFMGSLAEFFDIASQIQMLYLLLSLCMGWTIVRMKKSQSRPLQ |
| LL.L.AGSALANYI.FSSYS.DGIGVPFM.S.AEFFD...QIQM.YLLLSLCMGWTIVRMKKSQSRPLQ | |
| Retrocopy | LL<LMAGSALANYIYFSSYSKDGIGVPFM*SSAEFFDTTFQIQMSYLLLSLCMGWTIVRMKKSQSRPLQ |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 14 .04 RPM |
| SRP051959_heart | 0 .00 RPM | 12 .80 RPM |
| SRP051959_kidney | 0 .00 RPM | 13 .87 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .65 RPM |
| SRP051959_lung | 0 .00 RPM | 13 .97 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 13 .77 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 6 .60 RPM |
| SRP051959_spleen | 0 .00 RPM | 16 .87 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2708 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2708 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2708 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003277 | 1 retrocopy |
retro_cjac_2708 ,
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