RetrogeneDB ID:

retro_rnor_2770

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:X:7844189..7845266(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000046063
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Sdccag3
Ensembl ID:ENSRNOG00000018876
Aliases:None
Description:serologically defined colon cancer antigen 3 [Source:RefSeq peptide;Acc:NP_001013153]


Retrocopy-Parental alignment summary:






>retro_rnor_2770
GATTTTGGCTATGGAAAGGGGAAATGTACTAAACAAGGTCCGTCGGGAGCCCATGAGACGCGCTTTGGAGGTGACAAACT
TGAAGACCTTGAAGAAGCCAATCCATTCTCCTTCAAAGAGTTTTTGAAAACCAAGAACCTCAGCCTGTCAAAAGAAGACA
CAGCCACCAGTCGAATTTACCCGAAGGAGGCCTCGAGGCACCCACTGGGACTAGACCACAACTCCCCTGTCTCCCAGCCC
ATGGGATATGGCCTGGAATATCAGCAGCCATTTTTTGAAGACCCAACAAGAGCCAGCAACCTAGAGGAGGATGAAGAGGA
CGGGTGGAGCAGAGCCTACCTGCCGTCTGCCGTGGAGCAGACTCACTCCATGAGAGCCACGCAGAACTCATCGCCCTGTG
GCACCTACCTTTCCTTCTTTTCCAACGCGTCAGAGCTGGCAGGTCCTGAGTCTTTGCCCCCATGGACACTGAGTGACACT
GACTCCAGGCTCTCCCCAGCGTCTCCAGCTGGGAATCCTAATGTAGACTTTGCAGCTCATGAAGAATCCTTAGGGGACAG
ACACCTGCGGACGCTGCAGTTAAGTTACGAAGCACTGAAAGATGAAAACTCTAAGCTCAGAAGAAAGCTAAGTGAGGTTC
AGAGCTTCTCTGAAACTCAAACAAAAATGGTCAGGACGCTCGAACGGAAGTTGGAGGCGAAGATGATCAAGGAAGAGAGT
GACTTCCATGACCTGGAGTCAGTAGTCCAGCAAGTCGAACAGAACCTCGAACTGATGACCAAACGGGCTGTAAAAGCAGA
AAATCATGTCATGAAGCTGAAACAGGAAGTAAATTTGCTCCAGGCACAGCTCTCCAACTTCAAGCGAGAAAACGAAGCCC
TGCGGTCAGGCCAGGGTGCCAGCCTTACCGTGGTGAAGCAGAACACCGATGTGGCCTTGCAGAACCTCCATGTTGTCATG
AACAGTGCACACGCATCTATAAAGCAGCTGGTGTCTGGAGCAGAGACACTGAACCTTGTTGCTGAAATCCTCAAGTCTAT
CGACAGAATTACTGAAGTTAAGGATGAGGCAGACTCT

ORF - retro_rnor_2770 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.44 %
Parental protein coverage: 83.1 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDFGYGKGKCTKQGPSGAHETRFGGDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLG
DFGYGKGKCTKQGPSGAHETRFGGDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLG
RetrocopyDFGYGKGKCTKQGPSGAHETRFGGDKLEDLEEANPFSFKEFLKTKNLSLSKEDTATSRIYPKEASRHPLG
ParentalLDHNSPVSQPMGYGLEYQQPFFEDPTRASNLEEDEEDGWSRAYLPSAVEQTHSTRATQNSSPCGTYLSFF
LDHNSPVSQPMGYGLEYQQPFFEDPTRASNLEEDEEDGWSRAYLPSAVEQTHS.RATQNSSPCGTYLSFF
RetrocopyLDHNSPVSQPMGYGLEYQQPFFEDPTRASNLEEDEEDGWSRAYLPSAVEQTHSMRATQNSSPCGTYLSFF
ParentalSNASELAGPESLPPWTLSDTDSRLSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKL
SNASELAGPESLPPWTLSDTDSRLSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKL
RetrocopySNASELAGPESLPPWTLSDTDSRLSPASPAGNPNVDFAAHEESLGDRHLRTLQLSYEALKDENSKLRRKL
ParentalSEVQSFSETQTEMVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLL
SEVQSFSETQT.MVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLL
RetrocopySEVQSFSETQTKMVRTLERKLEAKMIKEESDFHDLESVVQQVEQNLELMTKRAVKAENHVMKLKQEVNLL
ParentalQAQLSNFKRENEALRSGQGASLTVVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRI
QAQLSNFKRENEALRSGQGASLTVVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRI
RetrocopyQAQLSNFKRENEALRSGQGASLTVVKQNTDVALQNLHVVMNSAHASIKQLVSGAETLNLVAEILKSIDRI
ParentalTEVKDEADS
TEVKDEADS
RetrocopyTEVKDEADS

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 .07 RPM 42 .49 RPM
SRP017611_kidney 0 .21 RPM 36 .15 RPM
SRP017611_liver 0 .00 RPM 22 .73 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2770 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2770 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2770 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001656891 retrocopy
Gorilla gorilla ENSGGOG000000109051 retrocopy
Mus musculus ENSMUSG000000269273 retrocopies
Nomascus leucogenys ENSNLEG000000081861 retrocopy
Otolemur garnettii ENSOGAG000000158721 retrocopy
Pongo abelii ENSPPYG000000197722 retrocopies
Pan troglodytes ENSPTRG000000215551 retrocopy
Rattus norvegicus ENSRNOG00000018876 2 retrocopies
retro_rnor_1215, retro_rnor_2770 ,



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