RetrogeneDB ID:

retro_rnor_2278

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:6:28503988..28504317(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000040044
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Znhit1
Ensembl ID:ENSRNOG00000001418
Aliases:None
Description:zinc finger, HIT domain containing 1 [Source:RefSeq peptide;Acc:NP_001258279]


Retrocopy-Parental alignment summary:






>retro_rnor_2278
CAGGCAGAGGCGGATCAACAGTTGGAGGTGTTAGAGAACAACTTCCAGGATGACCCCCACGCCGGCCTCCCCCAGCTGGG
CAAGAGACTACCTCAGTTCGATGATGATGCAGACACAGGAAAGAAAAAGAAGAAAACTCGAGGTGACCACTTCAAACTTC
GCTTACCCAAAAACTTCCAGGCTTTGCTGGAGGAGCAGAACCTGAATGCATCTGAGGGCCCCAACTACTTGACAGTCTGT
GTAGTTCCCCCATCTCGGCCCCAGCGTCCCTTCTGTGCTGGTGTGGCTTCCCATCCACGTATACCTGTGTAAGCTGTGGT
GCCCGGTAC

ORF - retro_rnor_2278 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.71 %
Parental protein coverage: 73.03 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalQRRINRQLEALENDNFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFKLRFRKNFQALLEEQNLS
Q.....QLE.LEN.NFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFKLR..KNFQALLEEQNL.
RetrocopyQAEADQQLEVLEN-NFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFKLRLPKNFQALLEEQNLN
ParentalASEGPNYLTACAGPPSRPQRPFCA-VCGFPSPYTCVSCGARY
ASEGPNYLT.C..PPSRPQRPFCA..CGFPS.YTCVSCGARY
RetrocopyASEGPNYLTVCVVPPSRPQRPFCA<WCGFPSTYTCVSCGARY

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 .14 RPM 15 .60 RPM
SRP017611_kidney 0 .00 RPM 10 .12 RPM
SRP017611_liver 0 .07 RPM 4 .71 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2278 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2278 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2278 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000101741 retrocopy
Homo sapiens ENSG000001064001 retrocopy
Gorilla gorilla ENSGGOG000000167131 retrocopy
Macaca mulatta ENSMMUG000000069511 retrocopy
Pan troglodytes ENSPTRG000000195251 retrocopy
Rattus norvegicus ENSRNOG00000001418 2 retrocopies
retro_rnor_2162, retro_rnor_2278 ,



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