RetrogeneDB ID:

retro_ptro_1860

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:13006551..13007614(-)
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:ENSPTRG00000004996
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1860
ATGAGCTTCACCAATCGCTCCACCTTCTCCACCAACTACTGGTCCCTGGGCTCTGTCCAGGTGCCAGCTATGGCGCCCGG
CTGGTCAGCAGCATGGTCAGCATCTCTGCAGTCGCTGGGGGCTCTGGTTCCCGGATCTCCGTGTCTCACTCCACCAGCTT
CCGGGGCGGCATGGGGTCCAGGGGCCTGGCCTCGGGGATGGCTGGGGGTCTGGCAGGAATGGGAGGCATCCAGAACAAGA
AGGAGACCATGCAAAGCCTGAACAACCACCTGGCCTCCTACCTGGACAGAGTGAGGAGCCTGGAGACCGAGAACTGGAGG
CTGGAGAGCAAAATCCAGGAGCACCTGGAGAAGAAGGGACCCCAGGTCAGAGACTGGAGCCATTGCTTCAAGACCATCGA
GGACCTGAGGGCTCAGATCTTCACAAATACTGTGGACAACGCCCGCATCGTTCTGCAGATCAACAATGCCCATCTTGCTG
CTGATGACTTTAGAGTCAAGTATGAGGCAGAGCTGGCCATGCGCCAGTCTGTGGAGAACGACACCATGGGCTCTGCAAGG
TCATTGATGACACCAATGTCACTCAGCTGCAGCTGGAGACAGAGATTGAGGCTCTCAAGGAGGAGCTGCTCTTCACGAAG
AAGAACCACGAAGAGGAAGTAAAAGGCCTACAAGCCCAGATTGCCAGCTCTGGGTTGACAGTGGAGGTAGATGCCCCCAA
ATCTCAGGACCTCACCAAGATCATGGCAGATATCCAAGCCCAATATGACAAGCTGGCTCAGAAGAACCAAGAGGAGCTGG
ACAAGTACTGGTCTCAGCAGATTGAGGAGAGCACCACAGTGGTCACCACGCAGTCCGTGGAGGTTGGAGCTGCTGAGATG
ATGCTCACAGAGCCGAGATGTACAGTCCAGTCCTTGGAGATCAAGCTGGACTCTGTGAGAAATCTGAAGCCCAGCTTGGA
GAACAGCCTGAGGGAGGTGGAGGCCCGCTACACCCTGCAGATAGAGCAGCTCAGCGGGATCCTGCTGCACCTGGAGCTGG
CACTGACTTGGGCAGAGGGACAG

ORF - retro_ptro_1860 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.79 %
Parental protein coverage: 83.02 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSFTTRSTFSTNYRSLGSVQAP-SYGARPVSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAG
MSFT.RSTFSTNY.SLGSVQ.P.SYGAR.VSS..S..A.AGGSGSRISVS.STSFRGGMGS.GLA.G.AG
RetrocopyMSFTNRSTFSTNYWSLGSVQVP<SYGARLVSSMVSISAVAGGSGSRISVSHSTSFRGGMGSRGLASGMAG
ParentalGLAGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQ
GLAGMGGIQN.KETMQSLN..LASYLDRVRSLETEN.RLESKI.EHLEKKGPQVRDWSH.FK.IEDLRAQ
RetrocopyGLAGMGGIQNKKETMQSLNNHLASYLDRVRSLETENWRLESKIQEHLEKKGPQVRDWSHCFKTIEDLRAQ
ParentalIFANTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVENDI-HGLRKVIDDTNITRLQLETEIEALKE
IF.NTVDNARIVLQI.NA.LAADDFRVKYE.ELAMRQSVEND..HGL.KVIDDTN.T.LQLETEIEALKE
RetrocopyIFTNTVDNARIVLQINNAHLAADDFRVKYEAELAMRQSVENDT<HGLCKVIDDTNVTQLQLETEIEALKE
ParentalELLFMKKNHEEEVKGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEES
ELLF.KKNHEEEVKGLQAQIASSGLTVEVDAPKSQDL.KIMADI.AQYD.LA.KN.EELDKYWSQQIEES
RetrocopyELLFTKKNHEEEVKGLQAQIASSGLTVEVDAPKSQDLTKIMADIQAQYDKLAQKNQEELDKYWSQQIEES
ParentalTTVVTTQSAEVGAAETTLTELRRTVQSLEIDLDSMRNLKASLENSLREVEARYALQMEQLNGILLHLESE
TTVVTTQS.EVGAAE..LTE.R.TVQSLEI.LDS.RNLK.SLENSLREVEARY.LQ.EQL.GILLHL..E
RetrocopyTTVVTTQSVEVGAAEMMLTEPRCTVQSLEIKLDSVRNLKPSLENSLREVEARYTLQIEQLSGILLHL--E
ParentalLAQTRAEGQ
LA.T.AEGQ
RetrocopyLALTWAEGQ

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 .14 RPM 0 .34 RPM
SRP007412_cerebellum 0 .00 RPM 3 .69 RPM
SRP007412_heart 0 .03 RPM 1 .63 RPM
SRP007412_kidney 0 .03 RPM 148 .80 RPM
SRP007412_liver 0 .00 RPM 385 .90 RPM
SRP007412_testis 0 .63 RPM 1 .26 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1860 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1860 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1860 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 325 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000119812 retrocopies
Canis familiaris ENSCAFG0000000715410 retrocopies
Callithrix jacchus ENSCJAG0000001816529 retrocopies
Cavia porcellus ENSCPOG000000026181 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
Nomascus leucogenys ENSNLEG0000001773245 retrocopies
Oryctolagus cuniculus ENSOCUG000000276911 retrocopy
Pongo abelii ENSPPYG0000000456360 retrocopies
Pan troglodytes ENSPTRG00000004996 58 retrocopies
Rattus norvegicus ENSRNOG000000473933 retrocopies



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