RetrogeneDB ID:

retro_pabe_1681

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:19:54337122..54337917(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ZNF860
Ensembl ID:ENSPPYG00000010353
Aliases:None
Description:zinc finger protein 860 [Source:HGNC Symbol;Acc:34513]


Retrocopy-Parental alignment summary:






>retro_pabe_1681
GTTTGTGACAAGGCTTTCGTACGTAATTCATACCTGGCAAGACATACCAGAATTCACACTGCGGAGAAACCTTACAAGTG
TAATGAATGTGGGAAGACTTTTAATCAACAATCACAATTTTCACTTCATCATAGAGTTCATGCTGGAGAGAAACTTTACA
AATGTGAAGCATGTGACAAAGTTTTCAGTCGTGAATCACACCTTAAAAGACATAAGAGAATTCATCCTGGAGACAACGCA
TACAAATGTAAGGTTTGTGACAAGACTTTTGGGAGTGATTCACACCTGAGACAACATACTGGAATTCACACTGGAGGGAA
ACCTTACAAGTGTAATGAGTGTGGCAAAGCCTTTAGCAAGCAGTCAACACTTATTCACCATCAGGCAGTTCATGGTGTAG
GGAAACTTGACTAATGTAATGATTGTCACAAAGTCTTCAGTAACGCTACAACCATTGCAAATCATTGGAGAATCTATAAT
GAATAGAGATCTAACAAGTGTAATAAATGTGGCAAATTTTTGAGACATCATTCACACATTGCAGTTCATTGACACACTCA
TACTGGAGAGAAACCTTACAAATGTCATGATTGAGGCAAGGTCTTCGGTCAAGCTTCATCCTATGCAAAACATAGGAGAA
TTCATACAGAAGAGAAACCTCACAAGTGTGATGATTGTGGCAAAGCCTTTACTTCACGTTCACACCTCATTAGACATCAG
AGAATCCCTACTGGACAGAAATCTTACAAATGTCATCAGTGTGGCAAGGTCTTCAGTCCGAGTTCACTCTTTGCG

ORF - retro_pabe_1681 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.49 %
Parental protein coverage: 51.26 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVCGKVFNQKRYLACHRRCHTGEKPYKCNDCGKTFSQELTLTCHHRLHTGEKPYKCEECDEAFSFKSNLER
VC.K.F....YLA.H.R.HT.EKPYKCN.CGKTF.Q......HHR.H.GEK.YKCE.CD..FS..S.L.R
RetrocopyVCDKAFVRNSYLARHTRIHTAEKPYKCNECGKTFNQQSQFSLHHRVHAGEKLYKCEACDKVFSRESHLKR
ParentalHRIIHTGEKLYKCNECGKTFSRKSSLTRHRRLHTGEKPYQCNECGKAFRGQSALIYHQAIHGIGKLYKCN
H..IH.G...YKC..C.KTF...S.L..H...HTG.KPY.CNECGKAF..QS.LI.HQA.HG.GKL..CN
RetrocopyHKRIHPGDNAYKCKVCDKTFGSDSHLRQHTGIHTGGKPYKCNECGKAFSKQSTLIHHQAVHGVGKLD*CN
ParentalDCHQVFSNATTIANHWRLHNEERLYKCNRCGKFFRHRSYLAVHWRTHSGEKPYKCNECGKTYSHNSVLVI
DCH.VFSNATTIANHWR..NE.R..KCN.CGKF.RH.S..AVH..TH.GEKPYKC...GK.....S....
RetrocopyDCHKVFSNATTIANHWRIYNE*RSNKCNKCGKFLRHHSHIAVH*HTHTGEKPYKCHD*GKVFGQASSYAK
ParentalHKTIHTGEKPYKCNECGKTFHHNSVLAIHKTIHTGEKPYKSNDCGEVFNQQAHLA
H..IHT.EKP.KC..CGK.F...S.L..H..I.TG.K.YK...CG.VF......A
RetrocopyHRRIHTEEKPHKCDDCGKAFTSRSHLIRHQRIPTGQKSYKCHQCGKVFSPSSLFA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 .11 RPM 1 .00 RPM
SRP007412_cerebellum 0 .36 RPM 4 .26 RPM
SRP007412_heart 0 .09 RPM 0 .93 RPM
SRP007412_kidney 0 .40 RPM 1 .23 RPM
SRP007412_liver 0 .43 RPM 0 .80 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1681 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1681 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1681 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Pongo abelii ENSPPYG00000010353 1 retrocopy
retro_pabe_1681 ,


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