RetrogeneDB ID:

retro_ptro_2717

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:8:121434840..121435716(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CDK5
Ensembl ID:ENSPTRG00000019872
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2717
ATGCAGAAATAAAAGAAACTGGAGAAGATTGGGGAAGGCACCTATGGGACAGTGTTCAAGGCCAAAAACTGGGAGACTCA
TGAGATTGTGGCTCTGAAATGGGTGAGGCTGGATGACAATGATGAGGGTGTGCCGAGTTCTGCCCTCCGGGAGATCTGCC
TACTCAAGGAGCTGAAGCACAAGAACATCGTCAGGCTTCATGACGTCCTGCACAGCGACAAGAAGCTGACTTTGGTTTTC
AAATTCTGTCACCAGCACCTGAAAAAGTATTTTGACAGTTGCAATGGTGACCTCGATCCTGAGATTGTAAAGTCATTTCT
CTTCCAGCTGCTAAAAGGCCTCGGATTCTGTCACAGCCGCAATGTGCTACGCAGGGACCTGAAGCCCCAGAACCTGCTAA
TAAACAGGAATGGGGAGCTGAAATTGGCTGACTTTGGCCTGTCTCGAGCCTTTGGGATCCCCATCTGCTGTTACTGAGCT
GGAGTGGTCACACTGTGGTACCACCCACCAGATGTCTTCTTTGGGGCCAAGCTGTACTCCACGTCCATTGACTTGTGGTC
AGCTGGCTGCATCTTTGCGGAGCTGGCCAATGCTGGATGGCCTCTTTTTCCAGGCAATGATGTCGATGACCAGTTGAAGA
GGATCTTCTGGCTGCTAGGGATGCTCACCAAGGAGCAGTGGCCCTCCATGACCAAGCTGCCAGACTATAAGCTGTACCCA
TTGTACCCGGCCACAACATCCCTGGTGAACATCGTGCCCAAACTCAATGCCACAGGGAGGGATCTGCTGCAGAATCTTCT
GAAGTGTAACCCCTGCCAATGTATCTCAGCAGAAGAGGCCCTGCAGCACCCCTACTTTTCCGACTTCTGTCCGCCC

ORF - retro_ptro_2717 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.75 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVL
MQK..KLEKIGEGTYGTVFKAKN.ETHEIVALK.VRLDD.DEGVPSSALREICLLKELKHKNIVRLHDVL
RetrocopyMQK*KKLEKIGEGTYGTVFKAKNWETHEIVALKWVRLDDNDEGVPSSALREICLLKELKHKNIVRLHDVL
ParentalHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGEL
HSDKKLTLVF.FC.Q.LKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVL.RDLKPQNLLINRNGEL
RetrocopyHSDKKLTLVFKFCHQHLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLRRDLKPQNLLINRNGEL
ParentalKLADFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDD
KLADFGL.RAFGIP..CY.A.VVTLWY.PPDV.FGAKLYSTSID.WSAGCIFAELANAG.PLFPGNDVDD
RetrocopyKLADFGLSRAFGIPICCY*AGVVTLWYHPPDVFFGAKLYSTSIDLWSAGCIFAELANAGWPLFPGNDVDD
ParentalQLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEA
QLKRIF.LLG..T.EQWPSMTKLPDYK.YP.YPATTSLVN.VPKLNATGRDLLQNLLKCNP.Q.ISAEEA
RetrocopyQLKRIFWLLGMLTKEQWPSMTKLPDYKLYPLYPATTSLVNIVPKLNATGRDLLQNLLKCNPCQCISAEEA
ParentalLQHPYFSDFCPP
LQHPYFSDFCPP
RetrocopyLQHPYFSDFCPP

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
SRP007412_brain_prefrontal_cortex 1 .43 RPM 51 .10 RPM
SRP007412_cerebellum 1 .72 RPM 22 .62 RPM
SRP007412_heart 0 .15 RPM 3 .15 RPM
SRP007412_kidney 0 .99 RPM 13 .63 RPM
SRP007412_liver 0 .69 RPM 7 .14 RPM
SRP007412_testis 0 .00 RPM 1 .69 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2717 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2717 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2717 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4002
Gorilla gorilla retro_ggor_2686
Pongo abelii retro_pabe_3290

Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000202581 retrocopy
Homo sapiens ENSG000001648851 retrocopy
Gorilla gorilla ENSGGOG000000168791 retrocopy
Nomascus leucogenys ENSNLEG000000041001 retrocopy
Pongo abelii ENSPPYG000000181831 retrocopy
Pan troglodytes ENSPTRG000000051471 retrocopy
Pan troglodytes ENSPTRG00000019872 1 retrocopy
retro_ptro_2717 ,
Ictidomys tridecemlineatus ENSSTOG000000160681 retrocopy



Copyright © RetrogeneDB 2014-2017