RetrogeneDB ID:

retro_cjac_2207

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:1074848..1075114(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CPSF4L
Ensembl ID:ENSCJAG00000019911
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2207
TTTGAAACAGACAATGAGATGCAAAAGGGCACTGGGCTCCCTTCTTTCCAGGGCATGGAGAAGTCGGACTCAGCTGTGTG
CAACTTCTTCACTAAAGGGCTCTGTGAGAAAGGGAAACTGTCCCTTCCCAGTATGACCGAGGGGACAAGATGGTGGTGTA
TAAGCACCAGCTCTGGGGGCTGTGCAACAGGGGCGACCACCATAAGTTCCTGCCTCAGTATGACCTCACCAGGATGCCCA
AGTGCTACTCCTACTGCAAGTTCGGT

ORF - retro_cjac_2207 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.22 %
Parental protein coverage: 53.94 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFETDVETQKGTGLLPFQGMDNEACPSCCLGPSALASPGKF-CPFWHDRGEKTVVCKHWLRGLCKKGDPCK
FETD.E.QKGTGL..FQGM.......C......L...GK...P...DRG.K.VV.KH.L.GLC..GD..K
RetrocopyFETDNEMQKGTGLPSFQGMEKSDSAVCNFFTKGLCEKGKL<VPSQYDRGDKMVVYKHQLWGLCNRGDHHK
ParentalFLHQCDLTRRPECCFYSTFG
FL.Q.DLTR.P.C..Y..FG
RetrocopyFLPQYDLTRMPKCYSYCKFG

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 0 .33 RPM
SRP051959_heart 0 .00 RPM 0 .42 RPM
SRP051959_kidney 0 .00 RPM 0 .40 RPM
SRP051959_liver 0 .00 RPM 0 .22 RPM
SRP051959_lung 0 .00 RPM 0 .42 RPM
SRP051959_lymph_node 0 .00 RPM 0 .48 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .35 RPM
SRP051959_spleen 0 .00 RPM 0 .44 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2207 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2207 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2207 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000019911 1 retrocopy
retro_cjac_2207 ,
Myotis lucifugus ENSMLUG000000096172 retrocopies
Monodelphis domestica ENSMODG000000256721 retrocopy



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