RetrogeneDB ID:

retro_pabe_2677

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:116535129..116535432(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CMC1
Ensembl ID:ENSPPYG00000014054
Aliases:None
Description:COX assembly mitochondrial protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28783]


Retrocopy-Parental alignment summary:






>retro_pabe_2677
GCCCAGCAGCAACTAAGATATGTCGAAAAAGATGTTCTGATGCCTAACATAATGAGAAAAATGGCCAGAGAGAGGTATTC
TGAAAAAGTTCAAGATTTTACCAAGTGTTGCAAGAACTCTAGAATCCTTATGGTGGTAAAATACTGGAAATACAATTCTG
CATTGAAAGACTGTCTTAACTGCTTACTATAATGATCCAGTCTTTTACAAAGAATACAAAATGGAATACCTGAAGGAATG
TAAGAACTCAGAAAAACTGGAATTTCTACCAAGTTAAAGCTACAGAAGCTTCCCATAAGCATG

ORF - retro_pabe_2677 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.84 %
Parental protein coverage: 95.28 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalADQHLRHVEKDVLIPKIMREKAKERCSEQVQDFTKCCKNSGVLMVVKCRKENSALKEC-LTAYYNDPAFY
A.Q.LR.VEKDVL.P.IMR..A.ER.SE.VQDFTKCCKNS..LMVVK..K.NSALK.C.LTAYYNDP.FY
RetrocopyAQQQLRYVEKDVLMPNIMRKMARERYSEKVQDFTKCCKNSRILMVVKYWKYNSALKDC>LTAYYNDPVFY
ParentalEECKMEYLKERE-EFRKTGIPAKKRLQKLPTSM
.E.KMEYLKE...E.RKTGI..K..LQKLP.SM
RetrocopyKEYKMEYLKECK<ELRKTGISTKLKLQKLPISM

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 3 .43 RPM
SRP007412_cerebellum 0 .00 RPM 6 .20 RPM
SRP007412_heart 0 .00 RPM 5 .39 RPM
SRP007412_kidney 0 .00 RPM 5 .34 RPM
SRP007412_liver 0 .00 RPM 6 .73 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2677 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2677 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2677 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3229
Pan troglodytes retro_ptro_2181
Gorilla gorilla retro_ggor_2196

Parental genes homology:
Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000042722 retrocopies
Dasypus novemcinctus ENSDNOG000000189232 retrocopies
Homo sapiens ENSG000001871184 retrocopies
Gorilla gorilla ENSGGOG000000124064 retrocopies
Microcebus murinus ENSMICG000000117022 retrocopies
Myotis lucifugus ENSMLUG000000000442 retrocopies
Nomascus leucogenys ENSNLEG000000040664 retrocopies
Oryctolagus cuniculus ENSOCUG000000127932 retrocopies
Ochotona princeps ENSOPRG000000094741 retrocopy
Pongo abelii ENSPPYG00000014054 4 retrocopies
Pan troglodytes ENSPTRG000000147064 retrocopies
Rattus norvegicus ENSRNOG000000101491 retrocopy
Sorex araneus ENSSARG000000016291 retrocopy
Tupaia belangeri ENSTBEG000000025734 retrocopies
Tarsius syrichta ENSTSYG000000113712 retrocopies



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