RetrogeneDB ID:

retro_pabe_2823

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5_random:9117343..9118129(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC176
Ensembl ID:ENSPPYG00000005979
Aliases:None
Description:coiled-coil domain containing 176 [Source:HGNC Symbol;Acc:19855]


Retrocopy-Parental alignment summary:






>retro_pabe_2823
CAGACAGAGCTGAAAAAAATAAACAAGAAAGAATGAGATGTTCTAAAGAAGAATTTAAAGAACAATTAATAGAAACATAA
GGAGACTGTTAGGACCTGGGAAGGCATGGTTTTTGAAGAAAATCATCGACTAGAACAAAAGGCTGAAAAAAGACAATGCT
GGCAATGAGGGCCCATCATGAAGTTGTCGTGCAATTGAACAATGACGGAAAAAAATGTGTTTAAAGGAACAATTATCTCC
AGAATGCTCTTGCATACCATCTGAAAGAAGTTTATGCTCTACAAAAACACTCCCAGAGATTGCAATAGAATCAAATCCTT
TTACATCAAAAGGAGATTAATGAGCTGTTGGTTAAGGAAAAGATTATGCAGCTTACCCAGTAGAAAACACAAATCCAAAC
ACTTCAGAAGAAGGTAGTAAGTTTGGAGACTGCTCTAAGTTATAGGACCAGAGTTTGAGACTGAAGCATTAAAACTGTAG
CAACAGCAATGATAGAGAACCAATCAGGTTACATATAAACTGACAAGCAGTAGCAAAGTCAGGTGAACAAAAGAAAAATG
AATTGAGTGAAGAAGCTGGCCAAGAACATACTAGGTGAGAGAACAGAATTGGACAGCTCTTTTTTAAATGCCCTACACCA
AGTGAAATAACAGATCCTATTTATCAGGAAGCATTTAAATTGAAAGCACAAGGGGCTTTCAATTACAAATGAGATCAGCA
CTTACAGGAAGAATGGAATATCCCCAAATCAGAACAATTGATGACAGAGAGCACAGCATCAATAGT

ORF - retro_pabe_2823 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.15 %
Parental protein coverage: 50.66 %
Number of stop codons detected: 12
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalQFQKRKIQVERELDDLKENLRNTERIHQETLRRLESRFFEEKHRLEQEAE-KKIIMLAERAHHEAIVQLN
Q....KI....E.D.LK.NL.N....H.ET.R..E...FEE.HRLEQ.AE.KK..MLA.RAHHE..VQLN
RetrocopyQTELKKIN-KKE*DVLKKNLKNN**KHKETVRTWEGMVFEENHRLEQKAE<KKT-MLAMRAHHEVVVQLN
ParentalDAGRNVFKENVYLQKALAYHLKETDALQKNSQKLQESHTLLLHQKEINDLLVKEKIMQLVQQRSQIQTLQ
..G......N.YLQ.ALAYHLKE..ALQK.SQ.LQ.....LLHQKEIN.LLVKEKIMQL.Q...QIQTLQ
RetrocopyNDGKKCV*RNNYLQNALAYHLKEVYALQKHSQRLQ*NQ-ILLHQKEINELLVKEKIMQLTQ*KTQIQTLQ
ParentalKKVVNLETALSYMTKEFESEVLKLQQHAMIENQAGQVEIDKLQHLLQMKDREMNRVKKLAKNILDERTEV
KKVV.LETALSY.T........K....AMIENQ.G....DK.Q...Q...R.MN.VKKLAKNIL.ERTE.
RetrocopyKKVVSLETALSYRTRV*D*SI-KTVATAMIENQSGYI*TDK-Q*QSQVNKRKMN*VKKLAKNILGERTEL
ParentalERFFLDALHQVKQQILISRKQ-YKQIAQAAFN-LKMRAACAGRTEYPKIRTFDGREHSTNS
...FL.ALHQVK.QIL..RK...K..AQ.AFN.L.MR.A..GR.EYP.IRT.D.REHS.NS
RetrocopyDSSFLNALHQVK*QILFIRKH<FKLKAQGAFN<LQMRSALTGRMEYPQIRTIDDREHSINS

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 .00 RPM 4 .31 RPM
SRP007412_cerebellum 0 .00 RPM 5 .72 RPM
SRP007412_heart 0 .00 RPM 1 .63 RPM
SRP007412_kidney 0 .00 RPM 5 .10 RPM
SRP007412_liver 0 .00 RPM 2 .39 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_2823 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2823 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2823 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 ENSPPYG00000005979 1 retrocopy
retro_pabe_2823 ,


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