RetrogeneDB ID:

retro_cjac_3743

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01198121.1:1258..1729(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MYL9
Ensembl ID:ENSCJAG00000012890
Aliases:None
Description:myosin, light chain 9, regulatory [Source:HGNC Symbol;Acc:15754]


Retrocopy-Parental alignment summary:






>retro_cjac_3743
CAGAGCAGCCCATCCAATGTCTTCGCGATGTTTGACCAGTTCCACATCCAGGAGTTCAAGGAGGCTTTCAACATGATTGA
CCAGAACTGTGAAGGCTTCGTTCACAAGGGGGACCTGAAGGACAAGCTGGCCTGACTGGGGAAGAACCCCAAGAATGAAT
ACCTGGAGAGTATAATAAGCAAGGCCCCGAGGCCCATCAACTTAACCACTTTCCTCACCATGTTTGGGAAGAAGCTGAAC
GGCAGGGACCCCAAGGATGTGATCCAAAATGCCTTTGCCTGCTTCAATTAGGAAGCCTCAGGTTTCTTCCATGAGGACCA
CCTCTGGGAGCTGCTCACCACCATGGGTGACAGCTTCACAGACGAGGAAGTGGATGAGATGTACCGGGAGGCACCCAATG
ATAAGAAGGGCAAGTTCAACTAGGTGGCGTTCACCCACATCCTCAAACATGGCTCCAACGACAAAGACGAC

ORF - retro_cjac_3743 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.8 %
Parental protein coverage: 91.28 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASLGKNPTDEYLEGMMSEAPGPINFTM
Q...SNVFAMFDQ..IQEFKEAFNMIDQN..GF..K.DL.D.LA.LGKNP..EYLE...S.AP.PIN.T.
RetrocopyQSSPSNVFAMFDQFHIQEFKEAFNMIDQNCEGFVHKGDLKDKLA*LGKNPKNEYLESIISKAPRPINLTT
ParentalFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVDEMYREAPIDKKGNFN
FLTMFG.KLNG.DP.DVI.NAFACF..EASGF.HEDHL.ELLTTMGD.FTDEEVDEMYREAP.DKKG.FN
RetrocopyFLTMFGKKLNGRDPKDVIQNAFACFN*EASGFFHEDHLWELLTTMGDSFTDEEVDEMYREAPNDKKGKFN
ParentalYVEFTRILKHGAKDKDD
.V.FT.ILKHG..DKDD
Retrocopy*VAFTHILKHGSNDKDD

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 38 .61 RPM
SRP051959_heart 0 .02 RPM 97 .23 RPM
SRP051959_kidney 0 .00 RPM 15 .00 RPM
SRP051959_liver 0 .00 RPM 3 .25 RPM
SRP051959_lung 0 .03 RPM 21 .73 RPM
SRP051959_lymph_node 0 .00 RPM 6 .21 RPM
SRP051959_skeletal_muscle 0 .00 RPM 10 .70 RPM
SRP051959_spleen 0 .00 RPM 15 .65 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3743 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3743 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3743 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000085403 retrocopies
Callithrix jacchus ENSCJAG00000012890 4 retrocopies
Callithrix jacchus ENSCJAG000000381512 retrocopies
Equus caballus ENSECAG000000075451 retrocopy
Homo sapiens ENSG000001013351 retrocopy
Gorilla gorilla ENSGGOG000000244771 retrocopy
Myotis lucifugus ENSMLUG000000002072 retrocopies
Nomascus leucogenys ENSNLEG000000061091 retrocopy
Pongo abelii ENSPPYG000000109711 retrocopy
Pan troglodytes ENSPTRG000000134581 retrocopy



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