RetrogeneDB ID:

retro_ocun_711

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:14:91826001..91826302(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PFDN6
Ensembl ID:ENSOCUG00000010559
Aliases:None
Description:prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]


Retrocopy-Parental alignment summary:






>retro_ocun_711
ATCCAGGGAGAAGTGGAGAAGCAGCAACAGCCACCCAAGGACTTGAGTAAGTCCACATCAGGGAGGCAGCAGCTTGAGCC
CAACTAACAGAAAGCAAGGTCGTGAGGAGGAGCTGGCTCTGCGCCACGGATCTAACGTGCTCTTTAAACTGCTGCCCCGG
GGCCGGTTAGGCAGGAGCTGGGGGAGGCTGGGCCACAGCGGGGAGGAGGCTGGACAGCATCACAACTGAAATCAAGCGAA
GCGAATCCCAGCTCCGGGACCTGGAACGCAGTCGGAGCAGCGGAGGGAGACCCCTGCTCAG

ORF - retro_ocun_711 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.96 %
Parental protein coverage: 79.07 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLQGEVEKYQQLQKDLSKSMSGRQKLE-AQLTENNIVK-EELALLDGSNVVFKLL-GPVLVKQELGEAR-A
.QGEVEK.QQ..KDLSKS.SGRQ.LE.AQLTE...V..EELAL..GSNV.FKLL..P..V.QELGEA..A
RetrocopyIQGEVEKQQQPPKDLSKSTSGRQQLE<AQLTESKVVR<EELALRHGSNVLFKLL<APGPVRQELGEAG<A
ParentalTVGKRLDYITAEIKRYESQLRDLER-QSEQQRETLAQ
T.G.RLD.IT.EIKR.ESQLRDLER.QSEQ.RET.AQ
RetrocopyTAGRRLDSITTEIKRSESQLRDLER<QSEQRRETPAQ

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 30 .52 RPM
SRP017611_kidney 0 .00 RPM 21 .08 RPM
SRP017611_liver 0 .00 RPM 6 .01 RPM
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_711 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_711 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_711 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 17 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000015762 retrocopies
Bos taurus ENSBTAG000000107231 retrocopy
Canis familiaris ENSCAFG000000009562 retrocopies
Cavia porcellus ENSCPOG000000195201 retrocopy
Dipodomys ordii ENSDORG000000138281 retrocopy
Felis catus ENSFCAG000000281991 retrocopy
Macropus eugenii ENSMEUG000000167781 retrocopy
Microcebus murinus ENSMICG000000009221 retrocopy
Mustela putorius furoENSMPUG000000023641 retrocopy
Mus musculus ENSMUSG000000243091 retrocopy
Oryctolagus cuniculus ENSOCUG00000010559 1 retrocopy
retro_ocun_711 ,
Otolemur garnettii ENSOGAG000000283414 retrocopies
Ochotona princeps ENSOPRG000000009831 retrocopy
Pteropus vampyrus ENSPVAG000000019101 retrocopy
Rattus norvegicus ENSRNOG000000004732 retrocopies
Sorex araneus ENSSARG000000063302 retrocopies
Tupaia belangeri ENSTBEG000000132801 retrocopy



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