RetrogeneDB ID:

retro_pabe_2797

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:172840969..172841936(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT18
Ensembl ID:ENSPPYG00000004563
Aliases:None
Description:keratin 18 [Source:HGNC Symbol;Acc:6430]


Retrocopy-Parental alignment summary:






>retro_pabe_2797
TTCACCACTCGCTTCACCTTCTCCACCAACTACCGGTCCCTGGGCTCCGTTCAGCCTCCCAGCTATGGTGCCCAGCCAGT
CAGCAGCACAGCCAGCGTCTATGCAGGCGCTGGGGGCTCAGGCTCCCAGATCTCTCTGTCCCACTCCACCAACTTTCAGG
GCAGCTTGGGGTCTGGGGGCCTGGCTGCGGGGCTGGCCGGGGGTCTGGAGAAAATGGGAGGCATCCAGAATGAGAAGGAG
ACCATGCAAAGCCTGAACGACTGCCTGGCCTCCTACCTGGACAGAGTGAGGAACCGGGAGACCGAGAACCAGAAGCTGGA
GAACAAAATCCGGGAGCACCTGGAGAAGAAGGGACCCCAGGTCAGAGACTGGGGCCATTACTTCAAGACCATCGAGGAAC
TGAGGACTCAGATCTTCACAAATACTGTGGACAATGCCCGCATCGTTCTGCAGATCAACAATGCCCATCTTGCTGCTGAT
GACTTTAGAGTCAAGTATGAGACAGGGCTGGCCATGCGCCAGTCTGTGGAGAGCCACATCCATGGGCTCCACAAAGTCAC
TGATGACACCAATGTCACTCGGCTGCAGCTGGAGACAGAGATCGAGGCTCTCAAGGAGGAGCTGCTCTTCATGAAGAAAA
ACCACAAAGAGGAAGTAAAAGGCCTACAAGCCCAGATTGCCAGCTCTGGGTTGGCCGTGGAGGTAGATGCCCCCAAATCT
CAGAACCTCACCAAGATCATGGCAGACATCCGGGCCCACTACAAGGAGCTGGCTCGGAAGAACCAAGAGGAGCTGGACAA
GTACTAGTCTCAGCAGACTGAGGAGAGCACCACAGTGGTCACCACACAGTCCGCCGAGGTTGAAGCTGCTGAGGTGACAA
TCAATGGAGCCGAGATTTACAATCCAGTCTTTGGAGATCGACCTGGACTCTATGAGAAATCTGAAAGCCAGCTTGGAGAA
CAGCCTG

ORF - retro_pabe_2797 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.52 %
Parental protein coverage: 74.88 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFTTRSTFSTNYRSLGSVQAPSYGARPVSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAGGLA
FTTR.TFSTNYRSLGSVQ.PSYGA.PVSS.ASVYAGAGGSGS.IS.S.ST.F.G..GSGGLA.G.AGGL.
RetrocopyFTTRFTFSTNYRSLGSVQPPSYGAQPVSSTASVYAGAGGSGSQISLSHSTNFQGSLGSGGLAAGLAGGLE
ParentalGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQIFA
.MGGIQNEKETMQSLND.LASYLDRVR..ETEN..LE.KIREHLEKKGPQVRDW.HYFK.IE.LR.QIF.
RetrocopyKMGGIQNEKETMQSLNDCLASYLDRVRNRETENQKLENKIREHLEKKGPQVRDWGHYFKTIEELRTQIFT
ParentalNTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNVTRLQLETEIEALKEELLF
NTVDNARIVLQI.NA.LAADDFRVKYET.LAMRQSVE..IHGL.KV.DDTNVTRLQLETEIEALKEELLF
RetrocopyNTVDNARIVLQINNAHLAADDFRVKYETGLAMRQSVESHIHGLHKVTDDTNVTRLQLETEIEALKEELLF
ParentalMKKNHEEEVKGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEESTTVV
MKKNH.EEVKGLQAQIASSGL.VEVDAPKSQ.L.KIMADIRA.Y.ELARKN.EELDKY.SQQ.EESTTVV
RetrocopyMKKNHKEEVKGLQAQIASSGLAVEVDAPKSQNLTKIMADIRAHYKELARKNQEELDKY*SQQTEESTTVV
ParentalTTQSAEVGAAETTLT-ELRRTVQSLEIDLDSMRNLKASLENSL
TTQSAEV.AAE.T...E.R.T.QSLEIDLDSMRNLKASLENSL
RetrocopyTTQSAEVEAAEVTIN>EPRFTIQSLEIDLDSMRNLKASLENSL

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 .05 RPM
SRP007412_cerebellum 0 .00 RPM 6 .20 RPM
SRP007412_heart 0 .00 RPM 1 .29 RPM
SRP007412_kidney 0 .00 RPM 50 .15 RPM
SRP007412_liver 0 .00 RPM 198 .51 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2797 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2797 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2797 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3400
Pan troglodytes retro_ptro_2310
Gorilla gorilla retro_ggor_2301

Parental genes homology:
Parental genes homology involve 21 parental genes, and 338 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000119812 retrocopies
Canis familiaris ENSCAFG0000000715410 retrocopies
Callithrix jacchus ENSCJAG0000001816529 retrocopies
Cavia porcellus ENSCPOG000000026181 retrocopy
Echinops telfairi ENSETEG000000081301 retrocopy
Homo sapiens ENSG0000011105760 retrocopies
Gorilla gorilla ENSGGOG0000001015728 retrocopies
Macropus eugenii ENSMEUG0000001226214 retrocopies
Myotis lucifugus ENSMLUG000000224398 retrocopies
Macaca mulatta ENSMMUG000000319114 retrocopies
Mustela putorius furoENSMPUG000000063692 retrocopies
Mus musculus ENSMUSG000000230432 retrocopies
Nomascus leucogenys ENSNLEG0000001773245 retrocopies
Oryctolagus cuniculus ENSOCUG000000276911 retrocopy
Pongo abelii ENSPPYG00000004563 60 retrocopies
Pan troglodytes ENSPTRG0000000499658 retrocopies
Pteropus vampyrus ENSPVAG000000093612 retrocopies
Rattus norvegicus ENSRNOG000000473933 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000155873 retrocopies
Tursiops truncatus ENSTTRG000000129772 retrocopies
Vicugna pacos ENSVPAG000000074213 retrocopies



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