RetrogeneDB ID:

retro_rnor_495

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:1:160387792..160388071(+)
Located in intron of:ENSRNOG00000033733
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Snrpc
Ensembl ID:ENSRNOG00000000493
Aliases:Snrpc, Snrp1c, U1-C, U1C
Description:U1 small nuclear ribonucleoprotein C [Source:UniProtKB/Swiss-Prot;Acc:D3ZCL3]


Retrocopy-Parental alignment summary:






>retro_rnor_495
CAAGGACAGATCCCTCCAGCTCCATCCTCTGCTCCTCTGCCTACTGGGGCCACAATCCCATCCCATCCCCAGTCTCCCGG
GTCCTCCTCTGCCTGACATGATGCCTGCATCCCACATGGGAGGCCCTCCCATGATGCCAACGATGGGCCCTCCTCCTCCT
GAGATGATACCTGTGGGACCAGCTTCCTGGGATGAGACTTCCCATGGGAGGACACATAACCATGATGCCCGGGGTCTCCA
ACGATGAGACCTCCCGCCCACCCTGGAATGACCCGCCCA

ORF - retro_rnor_495 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.26 %
Parental protein coverage: 55.29 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalQGKIPPAPFSAPPPAGAMIP-PPPSLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPA-PGMRPPM
QG.IPPAP.SAP.P.GA.IP.P.PSLPGPP.P.MMPA.HMGGPPMMP.MGPPPP.M.PVGPA.PGMR.PM
RetrocopyQGQIPPAPSSAPLPTGATIP>PIPSLPGPPLPDMMPASHMGGPPMMPTMGPPPPEMIPVGPA>PGMRLPM
ParentalGGHMPMM-PGPPMMRPPARPMMVPTRP
GGH..MM.PG.P.MRPPA.P.M..TRP
RetrocopyGGHITMM>PGSPTMRPPAHPGM--TRP

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 3 .16 RPM
SRP017611_kidney 0 .00 RPM 13 .12 RPM
SRP017611_liver 0 .00 RPM 5 .45 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_495 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_495 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_495 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 91 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000012313 retrocopies
Callithrix jacchus ENSCJAG0000001532116 retrocopies
Monodelphis domestica ENSMODG000000139041 retrocopy
Mus musculus ENSMUSG0000002421721 retrocopies
Nomascus leucogenys ENSNLEG000000083922 retrocopies
Oryctolagus cuniculus ENSOCUG000000266683 retrocopies
Otolemur garnettii ENSOGAG000000087559 retrocopies
Pongo abelii ENSPPYG000000172724 retrocopies
Rattus norvegicus ENSRNOG00000000493 30 retrocopies
Sarcophilus harrisii ENSSHAG000000009451 retrocopy
Sus scrofa ENSSSCG000000015311 retrocopy



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