RetrogeneDB ID:

retro_cjac_26

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:68198271..68199204(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023059
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000015659
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_26
AATAACTACTCCCACTTCCAACACCTTTACTTTGTCTTGACTGGAATTCCAGGGCTTGAGCAAAAGTACTATTGGATGGC
ATTCCCATTTGGTGCTATATATGTTGTTGCCCTCTTTGGCAATAGCATCATAATCTCTACCATCAAATCTGAGTCGTCTC
TACATATCCCTATGTACTACTTTCTGTGCATGCTGGCATTGGCAGACACGGGGCTTGCCCTCTGTACTTTGCCTTCTATG
CTAGGAATATTCTGGTTTAACTACAAGTCCATTGCCTTTGATGCCTGTCTTGTTCAGATGTACTTCATCCACACCTTCTC
AGCCATTGAGTCTGGGGTGCTGGTGGCAATGGCCTTTGATCGGGTTGTGGCAATCTGGAGCCCTCTCAGGTACAGTGTCA
TTCTAACCAATGGTGTGGTCTGCAAAACAGGGTTAGTCATCTTTTCAAGGGCAGTCTGTGTTGTCTTCCCTGTGCCTTTC
CTCATCAAGAGGCTCCCCTTCTACCACTCCAACATCCTCTCCCACTCCTTCTGCCTCCATCAAGATGTTATGCACCTTGC
CTGTGCCAGCACCCATGTCAACAGTCTCTATGGCCTCATCGCTGTCATCTTCACCAAGGGTTCTGACTCGCTATCCATCC
TTCTCTCCTATGTGTTTATACTTCGAACAGTAATGGCTATTGCCTCAAGGGAGGGTCGTCTGAAGGCACTCAACACCTGT
GTTTCACACATCTGTGCTGTACTCATCTTCTATGTGCCACTCATTGGGGTGTCTGTCATTCACCGCTTTGGAAAGCACCT
GTCACCACTGACTCATGTCCTCATGGCAAATGCCTACCTTCTTGTACCCCCTGTGCTAAACCCCATAGTCTATACTGTGA
AGACCAAAGAAATACGAAGGAAGATCATCCAGATATTTGTTCAAACCAAGATT

ORF - retro_cjac_26 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.64 %
Parental protein coverage: 98.39 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNSSEIEITTCFLIGIPGLEHAQVWISVPICLMYLVAIIGNCTILFVIRTEPSLHAPMYYFLSMLAVSDLG
N.S........L.GIPGLE....W...P....Y.VA..GN..I...I..E.SLH.PMYYFL.MLA..D.G
RetrocopyNYSHFQHLYFVLTGIPGLEQKYYWMAFPFGAIYVVALFGNSIIISTIKSESSLHIPMYYFLCMLALADTG
ParentalLSLSSLPTMLRIFVFNATGVSPNACFAQEFFIHGFTVMESSVLLVMSLDRFLAIRNSLRYSSILTNSVFI
L.L..LP.ML.IF.FN.......AC..Q..FIH.F...ES.VL..M..DR..AI...LRYS.ILTN.V..
RetrocopyLALCTLPSMLGIFWFNYKSIAFDACLVQMYFIHTFSAIESGVLVAMAFDRVVAIWSPLRYSVILTNGVVC
ParentalAIGIAIFTRAVCVVFPVPFLIKRLPFCHSNVLSHSYCLHQDMMRLACGSTHINSFYGLIVVIFTLGLDAL
..G..IF.RAVCVVFPVPFLIKRLPF.HSN.LSHS.CLHQD.M.LAC.STH.NS.YGLI.VIFT.G.D.L
RetrocopyKTGLVIFSRAVCVVFPVPFLIKRLPFYHSNILSHSFCLHQDVMHLACASTHVNSLYGLIAVIFTKGSDSL
ParentalLILMSYVLILKTVLGIASSGERLKTLSTCLSHMFAVLLFYVPFIGSSMIHRFGKHLPPVVHMLMANIYLL
.IL.SYV.IL.TV..IAS...RLK.L.TC.SH..AVL.FYVP.IG.S.IHRFGKHL.P..H.LMAN.YLL
RetrocopySILLSYVFILRTVMAIASREGRLKALNTCVSHICAVLIFYVPLIGVSVIHRFGKHLSPLTHVLMANAYLL
ParentalLPPVLNPIVYSVKTKQIRRRIIQVF
.PPVLNPIVY.VKTK.IRR.IIQ.F
RetrocopyVPPVLNPIVYTVKTKEIRRKIIQIF

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 0 .00 RPM
SRP051959_heart 0 .00 RPM 0 .00 RPM
SRP051959_kidney 0 .00 RPM 0 .00 RPM
SRP051959_liver 0 .00 RPM 0 .00 RPM
SRP051959_lung 0 .00 RPM 0 .00 RPM
SRP051959_lymph_node 0 .02 RPM 0 .00 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .00 RPM
SRP051959_spleen 0 .00 RPM 0 .00 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_26 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_26 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_26 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000015659 2 retrocopies
retro_cjac_25, retro_cjac_26 ,


Copyright © RetrogeneDB 2014-2017