RetrogeneDB ID:

retro_ptro_2277

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:78267045..78267999(-)
Located in intron of:ENSPTRG00000016801
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_2277
ATGAGCTTCACCACTTGCTCCACCTTCTCCACCAACTGCTGGTTCCTGGGCTCCGTCCAGCCACCCAGCTATGGTGCCTG
ACTGGTCAGCAGTGCAGCCAGCGTCTATGCAGGCGCCAGGGGCTCTGGTTCGCGGATCTCCGTGTCCTGTTCCACCAGCT
TCCGCGGCGGCTTGGGGTCCAGGGGCCTGGCCAAGTGGATGGCCCAGGGTCTGGCAGGAATGGGAGGCATCCAGAACAAG
GAGACCCTCCAAAGCCTGAACAACCACCTGGCCTCCTACCTGGACAGAGTGAGGAGCCTAGAGACCAAGAGCCAGAGACT
GGAGAGCAACACCCGGGAGCACCTGGAGAAGAAGGGACCCCAGGTCAGAGACTGGGGCCATTACTTCAAGACCATCGAGG
ATCTGAGGGCTCAGATCTTTGCAAATACTGTGGACAATGCCTACATTGTTGTGCAGATTGACAATGCCTGTCTTGCTGCT
GATGGCTTTAGAGTCAAGTGTGAGACAGAGCTGGCCATGTGCCAGTCTGTAGAGAACGACATCCGTGGGCTCTGCAAGGT
CATTGATGACACCAGTGTCACTTGGCTGTAGCTAGAGACAGACATCGAGGCTCTCAGGGAGGAGCTGCTCTTAATGAAGG
AGAACCACGAAGAGGAAGTAAAAGGCCTACAAGCCCAGCTCACCAGCTCTGGGTTGACCGTGAAGGTAGATGCTCCCAAA
TCTCAGGACCTCGCCAAGATCATGGCAGACATACAGGCCCAATACGACGAGCTAGCTCAGAAGAACCAAGAGGAGCTAGA
CAAGTACTGGTCTCAGCAGATTGAGGAGAGCACCACAGTGGTCACCACTCAGTCCGCGCAGGTCGGAGCTGCTGAGATGA
CACTCACGGAGCTGAGACATACGGTCCAGTCCTTGGAGATCCATCTGGACTTGATAAGAAATCTGAAGGCCAGC

ORF - retro_ptro_2277 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.07 %
Parental protein coverage: 74.19 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSFTTRSTFSTNYRSLGSVQAPSYGARPVSSAASVYAGAGGSGSRISVSRSTSFRGGMGSGGLATGIAGG
MSFTT.STFSTN...LGSVQ.PSYGA..VSSAASVYAGA.GSGSRISVS.STSFRGG.GS.GLA...A.G
RetrocopyMSFTTCSTFSTNCWFLGSVQPPSYGA*LVSSAASVYAGARGSGSRISVSCSTSFRGGLGSRGLAKWMAQG
ParentalLAGMGGIQNEKETMQSLNDRLASYLDRVRSLETENRRLESKIREHLEKKGPQVRDWSHYFKIIEDLRAQI
LAGMGGIQN.KET.QSLN..LASYLDRVRSLET...RLES..REHLEKKGPQVRDW.HYFK.IEDLRAQI
RetrocopyLAGMGGIQN-KETLQSLNNHLASYLDRVRSLETKSQRLESNTREHLEKKGPQVRDWGHYFKTIEDLRAQI
ParentalFANTVDNARIVLQIDNARLAADDFRVKYETELAMRQSVENDIHGLRKVIDDTNITRLQLETEIEALKEEL
FANTVDNA.IV.QIDNA.LAAD.FRVK.ETELAM.QSVENDI.GL.KVIDDT..T.L.LET.IEAL.EEL
RetrocopyFANTVDNAYIVVQIDNACLAADGFRVKCETELAMCQSVENDIRGLCKVIDDTSVTWL*LETDIEALREEL
ParentalLFMKKNHEEEVKGLQAQIASSGLTVEVDAPKSQDLAKIMADIRAQYDELARKNREELDKYWSQQIEESTT
L.MK.NHEEEVKGLQAQ..SSGLTV.VDAPKSQDLAKIMADI.AQYDELA.KN.EELDKYWSQQIEESTT
RetrocopyLLMKENHEEEVKGLQAQLTSSGLTVKVDAPKSQDLAKIMADIQAQYDELAQKNQEELDKYWSQQIEESTT
ParentalVVTTQSAEVGAAETTLTELRRTVQSLEIDLDSMRNLKAS
VVTTQSA.VGAAE.TLTELR.TVQSLEI.LD..RNLKAS
RetrocopyVVTTQSAQVGAAEMTLTELRHTVQSLEIHLDLIRNLKAS

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 .13 RPM 0 .34 RPM
SRP007412_cerebellum 0 .14 RPM 3 .69 RPM
SRP007412_heart 0 .15 RPM 1 .63 RPM
SRP007412_kidney 0 .08 RPM 148 .80 RPM
SRP007412_liver 0 .07 RPM 385 .90 RPM
SRP007412_testis 0 .11 RPM 1 .26 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2277 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2277 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2277 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3161
Pongo abelii retro_pabe_2628

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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