RetrogeneDB ID:

retro_cjac_3807

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL284720.1:57953..58560(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000003810
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3807
ATGGGTGCATACAAGTACATCCAGGAGCTGTAGGGAAAGAAGCAATCTGATGTCATGTGCTTTCTTCTGAGGGTCCGCTG
CTGGCAGTACCGTCAGCTCTCTGCTCTCCACAGGGCTCCCTGCCCCAACCGGCCTGATAAAGCACGCTGACTGGGCTACA
AGGCCAAGCAAGGTTACGTTATATATAGGATTCGTGTTCGCCATGGTGGCCGAAAACGCCCAGTTCCTAAGGGTACAACT
TACAGCAAGCCTGTCCATCATGGTGTTAACCAGCTGAAGTTTGCTCGAAGCCTTCAGTCTGTTGCAGAGGAGTGAGCTGG
ATGCCACTGTGGGGCTCTAAGAGTCCTGAATTCTTACTGGGTTGGCAAAGATTCCACATACAAATTTTTTTAGTTTATTC
TCATTGATCCATTCCATAAAGCTATCAGAAGAAATCCTGACACCCAGTGGATCACCAAACCAGTCCACAAACACAGGGAG
ATGCGTGGGCTGACATCTGCAGTCCAAAAGAGCTGTGGCCTTGGAAAGGGCCATAAGTTCCATCACTACTGGTGGTTCTC
GTCGGGCAGCTTGGAGAAAGCGCAATACTCTCCAGCTCCACCATTAC

ORF - retro_cjac_3807 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.73 %
Parental protein coverage: 99.51 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGG
MGAYKYIQEL..KKQSDVM.FLLRVRCWQYRQLSALHRAP.P.RPDKAR.LGYKAKQGYVIYRIRVR.GG
RetrocopyMGAYKYIQEL*GKKQSDVMCFLLRVRCWQYRQLSALHRAPCPNRPDKAR*LGYKAKQGYVIYRIRVRHGG
ParentalRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHK
RKRPVPKG.TY.KPVHHGVNQLKFARSLQSVAEE.AG.HCGALRVLNSYWVG.DSTYKFF..ILIDPFHK
RetrocopyRKRPVPKGTTYSKPVHHGVNQLKFARSLQSVAEE*AGCHCGALRVLNSYWVGKDSTYKFF*FILIDPFHK
ParentalAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFHH-TIGGSRRAAWRRRNTLQLHHY
AIRRNPDTQWITKPVHKHREMRGLTSA..KS.GLGKGHKFHH.T.G..R.AAWR.RNTLQLHHY
RetrocopyAIRRNPDTQWITKPVHKHREMRGLTSAVQKSCGLGKGHKFHH>TGGSRR-AAWRKRNTLQLHHY

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 .09 RPM 57 .58 RPM
SRP051959_heart 0 .16 RPM 53 .55 RPM
SRP051959_kidney 0 .02 RPM 53 .38 RPM
SRP051959_liver 0 .06 RPM 76 .16 RPM
SRP051959_lung 0 .02 RPM 50 .87 RPM
SRP051959_lymph_node 0 .09 RPM 60 .41 RPM
SRP051959_skeletal_muscle 0 .04 RPM 53 .94 RPM
SRP051959_spleen 0 .06 RPM 60 .46 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3807 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3807 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3807 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 84 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000034976 retrocopies
Callithrix jacchus ENSCJAG00000003810 23 retrocopies
Equus caballus ENSECAG000000101571 retrocopy
Loxodonta africana ENSLAFG000000041551 retrocopy
Procavia capensis ENSPCAG000000119951 retrocopy
Pongo abelii ENSPPYG0000001406518 retrocopies
Pan troglodytes ENSPTRG0000001469514 retrocopies
Pteropus vampyrus ENSPVAG0000000177113 retrocopies
Tursiops truncatus ENSTTRG000000072445 retrocopies
Vicugna pacos ENSVPAG000000085732 retrocopies



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