RetrogeneDB ID:

retro_ptro_1590

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2A:39382115..39383034(-)
Located in intron of:ENSPTRG00000011853
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ASS1
Ensembl ID:ENSPTRG00000021473
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1590
TCATCTGGCCTGTATGAGGACTGCTACCTCCTGGGCCCCTCTCTTCCCAGGCCTTACATCACCCGCAAACAAGTGGAAAT
TGCTCAGTGGGAGGGGGCAAAGTATGTGTCCCACAGTGCCATGGGAAAGGGGAACGATCAGGTCTGGTTTGAGCTCGCCT
GCTACTCGCTGGCCCCCCAGATTAAGGTCATTGCTCCTGGGAGGATCCCTGAGTTCTACAACCAGTCCAAGGGCCACAGT
GATCTGATGGAATATGCAGAGAAACATGGGATTCCCATCCCAGTCACTCTGAAGCACCCATGGAACATGGACGAGAACCT
CATGCACATCAGCCACGAGGCTGGAATCTTGGAGAACCCCAAGAACCAAGCACCTTCAGGTCTCTACATGAAGATTCAGG
ACCTGGCCAAAGCCCCCAACACCCCCAACATTTTCAAGACTGAGTAAAAAAGGGGTCCCTGTGAAGGTGACCAGCATCAA
GGATGGCACCACCCACCAGACCTCCTTGGTGCTCTTCATGTACCTGAATGAAGTCGCAGGCAAGCACAGCGTGGGCCATA
TTGACATCGTGGAGAACCGCTTCATTGAAATGAAGTCCTGAGGTATCTGCAAGACCCCAGCAGGCACCATCCTTTACCAC
CCTCATTTAGACATTGAGGGCTTTGCCATGGAACAGGAAGTGCGCAAAATCAAACAAGGCCTGGGCTTGAAATTTGCTGA
GTTGGTGTACACCGGTTTCTGGCACAACCCTCAGTGTGACTTTGCCCACCACTGCATTGCCAAGTCCCAGGACCGAGTGG
AAGGGAAAGTGCAGATATCCATCTTCAAGGGCCAGGTGTACATCCTCTGCCAGGAGCCCCCACTGTCTCTCTACAGTGGA
GAGCAGGTGAGCATGAACGTGCAGGGCAATGATGAGCCA

ORF - retro_ptro_1590 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.6 %
Parental protein coverage: 74.51 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSLAPHIKVIAPWRMP
SS.LYED.YLLG.SL.RP.I.RKQVEIAQ.EGAKYVSH.A.GKGNDQV.FEL.CYSLAP.IKVIAP.R.P
RetrocopySSGLYEDCYLLGPSLPRPYITRKQVEIAQWEGAKYVSHSAMGKGNDQVWFELACYSLAPQIKVIAPGRIP
ParentalEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTKTQDPAKA-P
EFYN..KG..DLMEYA..HGIPIPVT.K.PW.MDENLMHIS.EAGILENPKNQAP.GLY.K.QD.AKA.P
RetrocopyEFYNQSKGHSDLMEYAEKHGIPIPVTLKHPWNMDENLMHISHEAGILENPKNQAPSGLYMKIQDLAKA>P
ParentalNTPDILEIEFKKGVPVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRGIYETPAG
..P.......KKGVPVKVT..KDGTTHQTSL.LFMYLNEVAGKH.VG.IDIVENRFI.MKS.GI..TPAG
RetrocopyTPPTFSRLS-KKGVPVKVTSIKDGTTHQTSLVLFMYLNEVAGKHSVGHIDIVENRFIEMKS*GICKTPAG
ParentalTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKVQVSVLKGQ
TILYH.HLDIE.F.M..EVRKIKQGLGLKFAELVYTGFWH.P.C.F..HCIAKSQ.RVEGKVQ.S..KGQ
RetrocopyTILYHPHLDIEGFAMEQEVRKIKQGLGLKFAELVYTGFWHNPQCDFAHHCIAKSQDRVEGKVQISIFKGQ
ParentalVYILGRESPLSLYNEELVSMNVQGDYEP
VYIL..E.PLSLY..E.VSMNVQG..EP
RetrocopyVYILCQEPPLSLYSGEQVSMNVQGNDEP

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 .18 RPM 42 .11 RPM
SRP007412_cerebellum 0 .18 RPM 48 .83 RPM
SRP007412_heart 0 .09 RPM 16 .26 RPM
SRP007412_kidney 0 .29 RPM 1168 .07 RPM
SRP007412_liver 1 .28 RPM 933 .12 RPM
SRP007412_testis 0 .53 RPM 18 .44 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1590 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1590 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1590 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2247
Gorilla gorilla retro_ggor_1675
Pongo abelii retro_pabe_1963
Callithrix jacchus retro_cjac_1219

Parental genes homology:
Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000205543 retrocopies
Homo sapiens ENSG0000013070714 retrocopies
Gorilla gorilla ENSGGOG000000102288 retrocopies
Myotis lucifugus ENSMLUG000000060662 retrocopies
Mus musculus ENSMUSG000000764411 retrocopy
Nomascus leucogenys ENSNLEG0000001250013 retrocopies
Pongo abelii ENSPPYG0000001969213 retrocopies
Pan troglodytes ENSPTRG00000021473 14 retrocopies



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