RetrogeneDB ID:

retro_rnor_2704

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:9:99378917..99379163(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Phf5a
Ensembl ID:ENSRNOG00000024170
Aliases:Phf5a, Ac2-246
Description:PHD finger-like domain-containing protein 5A [Source:UniProtKB/Swiss-Prot;Acc:P83871]


Retrocopy-Parental alignment summary:






>retro_rnor_2704
ATGGCTAAACATCATCCAGATTTGATTTTCTGCCGCAGGCAGGCTGGTGTTGCTATTGGAAGACTGTGTGAAAAATGTGA
TGGCAAATGTGTGATCTGTGAATCCTACATGCGTCCCTGCACCCTGGTTCGCATATGTGATGAGTGTAACTATGGATCCT
ACCAGGGCCTCTGTGTGATCTGTGGAGGTCCCGGAGTCTCTGATGCCTACAATTGTAAAGAGTGCACCATTCAGGAGAAG
GATAGA

ORF - retro_rnor_2704 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.9 %
Parental protein coverage: 74.55 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAKHHPDLIFCRKQAGVAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGGPGVSDAY
MAKHHPDLIFCR.QAGVAIGRLCEKCDGKCVIC.SY.RPCTLVRICDECNYGSYQG.CVICGGPGVSDAY
RetrocopyMAKHHPDLIFCRRQAGVAIGRLCEKCDGKCVICESYMRPCTLVRICDECNYGSYQGLCVICGGPGVSDAY
ParentalYCKECTIQEKDR
.CKECTIQEKDR
RetrocopyNCKECTIQEKDR

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 .00 RPM 12 .65 RPM
SRP017611_kidney 0 .00 RPM 20 .66 RPM
SRP017611_liver 0 .00 RPM 11 .03 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_2704 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_2704 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_2704 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 20 parental genes, and 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000156871 retrocopy
Canis familiaris ENSCAFG000000010901 retrocopy
Callithrix jacchus ENSCJAG000000049993 retrocopies
Echinops telfairi ENSETEG000000107411 retrocopy
Homo sapiens ENSG000001004103 retrocopies
Gorilla gorilla ENSGGOG000000011042 retrocopies
Latimeria chalumnae ENSLACG000000120941 retrocopy
Microcebus murinus ENSMICG000000135201 retrocopy
Macaca mulatta ENSMMUG000000113543 retrocopies
Mustela putorius furoENSMPUG000000163982 retrocopies
Mus musculus ENSMUSG000000613603 retrocopies
Nomascus leucogenys ENSNLEG000000154812 retrocopies
Oryctolagus cuniculus ENSOCUG000000127051 retrocopy
Otolemur garnettii ENSOGAG000000028391 retrocopy
Pongo abelii ENSPPYG000000118702 retrocopies
Pan troglodytes ENSPTRG000000144273 retrocopies
Pteropus vampyrus ENSPVAG000000011621 retrocopy
Rattus norvegicus ENSRNOG00000024170 3 retrocopies
retro_rnor_2660, retro_rnor_2704 , retro_rnor_2712,
Tarsius syrichta ENSTSYG000000010821 retrocopy
Tursiops truncatus ENSTTRG000000033691 retrocopy



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