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:

ParentalLRLLAVALTCCWWPQGSQGKTLRGSFSSTVAQDAQGQRIGHFEFHGDHALLCVRINNIAVAVGKEAKLYL
L.LL.VALTCCWWPQ.SQ.KTL.GSFS.T.AQDA.GQ.I..F.FHGDHALLCVRINN...AV.K.AK.YL
RetrocopyLWLLVVALTCCWWPQSSQSKTLFGSFSNTAAQDAEGQHICRFKFHGDHALLCVRINNTDIAVEKQAKPYL
ParentalFQAQEWLKLQESSHGYSCSEKLSKAQLTMTMNQTEHNLTVSQIPSPQTWHVFYADKYTCQDDKENSQVED
FQAQEW.KLQ.SSHGYSCS.KLSK..LTMTMNQT.HNLTVSQIPS.QTWH.FY.DKYTCQDDK...QV..
RetrocopyFQAQEWIKLQKSSHGYSCSKKLSKV*LTMTMNQTKHNLTVSQIPSLQTWHGFYVDKYTCQDDKD-TQVDN
Parental-IPFEMVLLNPDAEGNPFDHFSAGESGLHEFFFLLVLVYFVIACIYAQSLWQAIKKGGPMHMILKVLTTA
..PFEMVLLNPDA.GN.FDHF.AGESGL.EFFFLLVLVYFVIACIYAQSL.QAIKKG.PMHMILKVL.TA
Retrocopy<YPFEMVLLNPDAKGNSFDHFTAGESGLPEFFFLLVLVYFVIACIYAQSL*QAIKKGRPMHMILKVLPTA
ParentalLL-LQAGSALANYIHFSSYSRDGIGVPFMGSLAEFFDIASQIQMLYLLLSLCMGWTIVRMKKSQSRPLQ
LL.L.AGSALANYI.FSSYS.DGIGVPFM.S.AEFFD...QIQM.YLLLSLCMGWTIVRMKKSQSRPLQ
RetrocopyLL<LMAGSALANYIYFSSYSKDGIGVPFM*SSAEFFDTTFQIQMSYLLLSLCMGWTIVRMKKSQSRPLQ

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_2708 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

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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