RetrogeneDB ID:

retro_pabe_1942

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2a:36397638..36398634(+)
Located in intron of:ENSPPYG00000012282
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_1942
ATGAGGAGCCTGGAGACTGAGAACAGGAAGCTGGAGAGCAAAATCTGGGAGCACCTGGAGAAGAAGGGACCCCAGGTCAG
AGACTGGAGCCATTACTTCAAGACCATTGAAGACATGAGCGCTCAGATCTTTGCAAATACTGTGGACAATGCCCACGTTG
TTGTGCAGATCGACAATGCCTGTCTTGCTGCTGGTGACTTTAGAGTCAACTATGAGATAGAGCTGGCCATGCGCTAGTCT
GTAAAGAGCAACATCCGTGGGCTCCACAAGGTCATTGATGACACCAGTGTCACTTGGCTGCAGCTGGAGACAGAGATCGA
GGCTCTCAAGGAGGAGCTGCTCTTCATGAAGAAGAACCATGAAGAGGAAGTAAAAGGCCTACAAGCCCAGATTACCAGCT
CTGGGTTGACCATGGAGGTAGATGCCCCCAAATCTTAGGACGTTGACAAGATCATGGCAGACACCTGGGCCCAATATGAC
TAGCTGGCTCAGAAGAGCTGAGAGGAGCCGGACAAGTACTGGTCTCAGCAGATGGAGGAGAGCACCACAGTGGTCACCAT
GCAGTCTGCCAAGGTTGGAGCTGCTGAGATGATGCTCATGAAACTGAGATGTACAGTCCAGTCCTTGGAGACTGACCTGG
TCTCCATGAGAAATCTGAAGGCCAGCTTGCAAAATAGCCTGAGGGAGGTGGAGGCCCACTACACCCTGCAGATGGAGCAG
CTCAATGGGATCCTGCTGCACCTGGAGTCAGAGCTGGCACAGACCCAGGCAGAAGGACAGTGCCAGGCCCAGGAGTACAA
GGCCCTGCTGAACATCAAGCTCAAGCTGGAGGCTGAGATGACCACCTACCACTGCCTGCTGGAAGATGGTGAGGACTTCA
ATCTTGGTGATGCCCTGGACAGCAGCTCCGTGCAAATCATCCAAAAGACCACTACCCACTGGATATTGGATGGCAAAGTG
GTGTCTGAGAATAATGACACCAAAGTTCTGAGACAT

ORF - retro_pabe_1942 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.68 %
Parental protein coverage: 77.44 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQIFANTVDNARIVLQIDNARLAADDFRVK
.RSLETENR.LESKI.EHLEKKGPQVRDWSHYFK.IED..AQIFANTVDNA..V.QIDNA.LAA.DFRV.
RetrocopyMRSLETENRKLESKIWEHLEKKGPQVRDWSHYFKTIEDMSAQIFANTVDNAHVVVQIDNACLAAGDFRVN
ParentalYETELAMRQSVENDIHGLRKVIDDTNVTRLQLETEIEALKEELLFMKKNHEEEVKGLQAQIASSGLTVEV
YE.ELAMR.SV...I.GL.KVIDDT.VT.LQLETEIEALKEELLFMKKNHEEEVKGLQAQI.SSGLT.EV
RetrocopyYEIELAMR*SVKSNIRGLHKVIDDTSVTWLQLETEIEALKEELLFMKKNHEEEVKGLQAQITSSGLTMEV
ParentalDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEESTTVVTTQSAEVGAAETTLTELRRTVQSLE
DAPKS.D..KIMAD..AQYD.LA.K..EE.DKYWSQQ.EESTTVVT.QSA.VGAAE..L..LR.TVQSLE
RetrocopyDAPKS*DVDKIMADTWAQYD*LAQKS*EEPDKYWSQQMEESTTVVTMQSAKVGAAEMMLMKLRCTVQSLE
ParentalIDLDSMRNLKASLENSLREVEARYALQMEQLNGILLHLESELAQTRAEGQRQAQEYEALLNIKVKLEAEI
.DL.SMRNLKASL.NSLREVEA.Y.LQMEQLNGILLHLESELAQT.AEGQ.QAQEY.ALLNIK.KLEAE.
RetrocopyTDLVSMRNLKASLQNSLREVEAHYTLQMEQLNGILLHLESELAQTQAEGQCQAQEYKALLNIKLKLEAEM
ParentalATYRRLLEDGEDFNLGDALDSSNSMQTIQKTTTRRIVDGKVVSETNDTKVLRH
.TY..LLEDGEDFNLGDALDSS.S.Q.IQKTTT..I.DGKVVSE.NDTKVLRH
RetrocopyTTYHCLLEDGEDFNLGDALDSS-SVQIIQKTTTHWILDGKVVSENNDTKVLRH

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 .03 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_1942 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1942 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1942 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2276
Pan troglodytes retro_ptro_1610
Gorilla gorilla retro_ggor_1692

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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