RetrogeneDB ID:

retro_ptro_2181

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:115985254..115985551(+)
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:ENSPTRG00000014706
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2181
CAGCAACTAAGACATGTCGAAAAAGATGTTCTGATGCCTAACATAATGAGAAAAATGGCCAGAGAGAGGTATTCTGAAAA
AGTTCAAGATTTTACCAAGTGTTGCAAGAACTCTGGAATCCTTATGGTGGTGAAATACTGGAAATAAAATTCTGCATTGA
AAGACTGTCTTAACTGCTTACTATAATGATCCAGTCTTTTACAAAGAATACAAAATGGAATACCTGAAGGAATGTAAGAA
CTCAGAAAAACTGGAATTTCTACTAAGTTAAAGCTACAGAAGCTTCCCATAAGCATG

ORF - retro_ptro_2181 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.24 %
Parental protein coverage: 93.4 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQHLRHVEKDVLIPKIMREKARERCSEQVQDFTKCCKNSGVLMVVKCRKENSALKEC-LTAYYNDPAFYEE
Q.LRHVEKDVL.P.IMR..ARER.SE.VQDFTKCCKNSG.LMVVK..K.NSALK.C.LTAYYNDP.FY.E
RetrocopyQQLRHVEKDVLMPNIMRKMARERYSEKVQDFTKCCKNSGILMVVKYWK*NSALKDC>LTAYYNDPVFYKE
ParentalCKMEYLKERE-EFRKTGIPTKKRLQKLPTSM
.KMEYLKE...E.RKTGI.TK..LQKLP.SM
RetrocopyYKMEYLKECK<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 2 .95 RPM
SRP007412_cerebellum 0 .00 RPM 1 .72 RPM
SRP007412_heart 0 .00 RPM 7 .32 RPM
SRP007412_kidney 0 .00 RPM 6 .80 RPM
SRP007412_liver 0 .00 RPM 6 .45 RPM
SRP007412_testis 0 .11 RPM 9 .17 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2181 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2181 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2181 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3229
Gorilla gorilla retro_ggor_2196
Pongo abelii retro_pabe_2677

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 ENSPPYG000000140544 retrocopies
Pan troglodytes ENSPTRG00000014706 4 retrocopies
Rattus norvegicus ENSRNOG000000101491 retrocopy
Sorex araneus ENSSARG000000016291 retrocopy
Tupaia belangeri ENSTBEG000000025734 retrocopies
Tarsius syrichta ENSTSYG000000113712 retrocopies



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