RetrogeneDB ID:

retro_ocun_342

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:1:15214104..15214648(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000023271
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000015632
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_342
CCTTGGGATTCGGAGGATGTAAAAGGACTTAGAATATCAGCTATTCGGGATAACAATCCAGTGGTGGGGTAGAGAATGAA
TTGATGTATGACATTCCTTTGGAACTTCCTGCTGAAGCTCAGTCAAAAGATTTTCTGATTCCTATCGGAAAAGCCAAAAT
AGAATGCCAAGGGACACACGTAACCGTGGTTGCCCATTCGAGACTTGTGGGCCACTGTTTAGAAGCTGGGACATTATTTT
CTAAAGAGGGAGTTGAATGTGAGGTCACAGGTCTGCGTACCATCAGACCAATGGATGTTGAAGCCACAGAAGGCAGCGCC
ATGAAAACAAGTCATCTGGTAACAGTGGAAGGAGGCTGGCCACAGTTTGGAGATGGAGCTGAAAGTTGTGCTAGTGTCAT
GGAAGGCCCTGCACTCAATGTCCTGGATGCACCTGCTGTCTGTGTCACTGGTACTGACCTCCCTCGGCCGTATACAGATT
CTTGAAGACATCTATACCTCAGGTCAAAGACATCATACTTGCAATAAAGAAAACATTAGACATC

ORF - retro_ocun_342 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.68 %
Parental protein coverage: 50.97 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPWNSEDAKGLIKSAIRDNNPVVV-LENELMYGVPFELPAEAQSKDFLIPIGKAKIERQGTHITVVAHSRP
PW.SED.KGL..SAIRDNNPVV...ENELMY..P.ELPAEAQSKDFLIPIGKAKIE.QGTH.TVVAHSR.
RetrocopyPWDSEDVKGLRISAIRDNNPVVG<VENELMYDIPLELPAEAQSKDFLIPIGKAKIECQGTHVTVVAHSRL
ParentalVGHCLEAATVLSKEGVECEVINLRTIRPMDIETIEASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAF
VGHCLEA.T..SKEGVECEV..LRTIRPMD.E..E.S.MKT.HLVTVEGGWPQFG.GAE.CA..MEGPA.
RetrocopyVGHCLEAGTLFSKEGVECEVTGLRTIRPMDVEATEGSAMKTSHLVTVEGGWPQFGDGAESCASVMEGPAL
ParentalNFLDAPAVRVTGADV-PMPYAKILEDNSIPQVKDIIFAIKKTLNI
N.LDAPAV.VTG.D..P......L...SIPQVKDII.AIKKTL.I
RetrocopyNVLDAPAVCVTGTDL<PSAVYRFLK-TSIPQVKDIILAIKKTLDI

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 85 .21 RPM
SRP017611_kidney 0 .00 RPM 123 .45 RPM
SRP017611_liver 0 .00 RPM 21 .27 RPM
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_342 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_342 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_342 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000217241 retrocopy
Canis familiaris ENSCAFG000000073402 retrocopies
Callithrix jacchus ENSCJAG000000197391 retrocopy
Dasypus novemcinctus ENSDNOG000000069371 retrocopy
Monodelphis domestica ENSMODG000000023981 retrocopy
Mus musculus ENSMUSG000000217481 retrocopy
Oryctolagus cuniculus ENSOCUG00000015632 1 retrocopy
retro_ocun_342 ,
Procavia capensis ENSPCAG000000165951 retrocopy
Sarcophilus harrisii ENSSHAG000000084801 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000195532 retrocopies
Tupaia belangeri ENSTBEG000000161482 retrocopies



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