RetrogeneDB ID:

retro_rnor_2150

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:5:72304911..72305616(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cnppd1
Ensembl ID:ENSRNOG00000018325
Aliases:Cnppd1, RGD735175
Description:Protein CNPPD1 [Source:UniProtKB/Swiss-Prot;Acc:Q6P7B2]


Retrocopy-Parental alignment summary:






>retro_rnor_2150
CTCTACACTGATCCTCGGGAGATCTTTGAGGTGCTGAGTTGGCTGGAGAGTTGTGTGCCTGAGCAGCAAGGACGGCGGCG
GGGCTGGTACACCTACACAGACCTGTGTGTGCTGCTGGAGCAGCCAATGTGGCAGCTCTCTCTGGGCTCCCTCTGCCAGC
GGCTGGTAAAGCTGTCCTGCCTATTAGCCATGGCATATGTGAGCAGTGTGGCCCTGGCTGTGGCATTCGTGGCTGTAATA
CACTAGTCCTTGGGTCTGTCCTCCAGCCCCTCACCAAGTCCTCCTGAACTCACACTGGTCCCCAAGAACCTCTTGCAGCC
CTGCATACCTGCCCCTGTGCCACAGTGCCTGACTAATGTCTCCAGCTGCCTGGAAGACAGTGTAGAGTTGCCGTCGCTCT
GGGGCAGTCTTCTGGACCCATTGACACCCCCTCTGATGCCTCCTCCAGACCCTCCTGCCCCACCTACTCCTTTCCACAAA
TGCCCCTTTTGCCAGAAGTTCCAGAGAAACCCCCCAAATTGCCGTGCCTGTCACCAGCCTAACCGTACAGTGTCTATTGA
TCCTATCCACCCCTTTTACCATACCCATGGCCTGGCCCCACCCTGGGTCTGGAGCCCAGTGGCCCCTCCATTCCTCCAGC
CCCAGCAGTGTTCTCTTTTTAGTGTCATGAAGCTGGCTCGCCTCACGTCTGTTATTTTCCCAGGC

ORF - retro_rnor_2150 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.02 %
Parental protein coverage: 57.6 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLYTDPREIFEVLSWLESCVAEQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLAVAYVSSV
LYTDPREIFEVLSWLESCV.EQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLA.AYVSSV
RetrocopyLYTDPREIFEVLSWLESCVPEQQGRRRGWYTYTDLCVLLEQPMWQLSLGSLCQRLVKLSCLLAMAYVSSV
ParentalALAVASMAVIHQSLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP
ALAVA..AVIH.SLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP
RetrocopyALAVAFVAVIH*SLGLSSSPSPSPPELTLVPKNLLQPCIPAPVPQCLTNVSSCLEDSVELPSLWGSLLDP
ParentalLTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSIGPIHPFYHTHGLAPPWLWSPVAPP
LTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSI.PIHPFYHTHGLAPPW.WSPVAPP
RetrocopyLTPPLMPPPDPPAPPTPFHKCPFCQKFQRNPPNCRACHQPNRTVSIDPIHPFYHTHGLAPPWVWSPVAPP
ParentalFLQPQQCSLFSVMKLARLTSVIFPG
FLQPQQCSLFSVMKLARLTSVIFPG
RetrocopyFLQPQQCSLFSVMKLARLTSVIFPG

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
SRP017611_brain 0 .72 RPM 27 .46 RPM
SRP017611_kidney 2 .79 RPM 56 .52 RPM
SRP017611_liver 2 .08 RPM 28 .91 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2150 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2150 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2150 has 0 orthologous retrocopies within eutheria group .


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

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG000000153281 retrocopy
Pteropus vampyrus ENSPVAG000000107861 retrocopy
Rattus norvegicus ENSRNOG00000018325 1 retrocopy
retro_rnor_2150 ,



Copyright © RetrogeneDB 2014-2017