RetrogeneDB ID:

retro_ptro_2490

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:140030822..140031592(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MTCH1
Ensembl ID:ENSPTRG00000018115
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2490
CCAAACACAAAGCCTTACGTGCTGGGGAGGAAGGTCCTCTATCTGCCAAGCTTCTTCACCTACGCCAAATACATTGTGCA
AGTGGATGGTAAGATAGGGCTGTTCCAAGGCCCGAGGCCCCAGCTGATGTCCAACGCCCTCTTCACTGTGACCCGGGTAG
CATGAAGAAGGCTTTTCCTCTAGATGAGATCTAGCAGGTTTCCAACAAGGGTGGTATGAAGACTTCCCTGAAGAAAGTTG
TGAAGGAGACCTCCTATGGGATAATGATGCAGTGCGTGTCCCGCATGTTGACCCACCCCCTGCATGTCATCTCAATGTGC
TGGATGGTCCAGTTTGTGGGATGGGAAGCCAAGGACAGTGGCGTGCTGAGCTCCATTGAGAAGCTTTTCAAAGAGGAAGG
GCTGCTGGGATTTGTTGGATTAATCCCTCACCTCCTGGGTGATGTGGTTTTCTTGTGAGGCTGTAACCTACTGGCCTACT
TCATCAGTGCCTACCTGGTGGATGACAGCCTCCACCAGGCCCTGGCCATCCGGAGCCACACCAAATGCTTGACAGGGATT
GCAGTAAGCATGCTGACCTACCCCTTCCTGCTAGTCGGCGACCTCATGGCTGTGAACAACTGTGGGCCGCAGGCTGGGCT
CCCCCGTTACTCCCCGGTGTTCAAATCCTGGATTCACTGCTGGAAGTACCTGAGTATGTAGGGCCAGCTCTTCCAAGGCT
CCAGCCTGCTTTTCCACTGGGTGTCATCAGGATCACCTTTCACCCTGGAG

ORF - retro_ptro_2490 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.01 %
Parental protein coverage: 69.35 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPTLGTNVLGRKVLYLPSFFTYAKYIVQVDGKIGLFRGLSPRLMSNALSTVTR-GSMKKVFPPDEIEQVSN
P.....VLGRKVLYLPSFFTYAKYIVQVDGKIGLF.G..P.LMSNAL.TVTR.GSMKK.FP.DEI.QVSN
RetrocopyPNTKPYVLGRKVLYLPSFFTYAKYIVQVDGKIGLFQGPRPQLMSNALFTVTR<GSMKKAFPLDEI*QVSN
ParentalKDDMKTSLKKVVKETSYEMMMQCVSRMLAHPLHVISMRCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFF
K..MKTSLKKVVKETSY..MMQCVSRML.HPLHVISM..MVQFVG.EAK.SGVLSSI.K.FKEEGLLGF.
RetrocopyKGGMKTSLKKVVKETSYGIMMQCVSRMLTHPLHVISMCWMVQFVGWEAKDSGVLSSIEKLFKEEGLLGF-
ParentalVGLIPHLLGDVVFLWGCNLLAHFINAYLVDDSFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLMAVNNC
VGLIPHLLGDVVFL.GCNLLA.FI.AYLVDDS..QALAIRS.TK...GIAVSMLTYPFLLVGDLMAVNNC
RetrocopyVGLIPHLLGDVVFL*GCNLLAYFISAYLVDDSLHQALAIRSHTKCLTGIAVSMLTYPFLLVGDLMAVNNC
ParentalGLQAGLPPYSPVFKSWIHCWKYLSVQGQLFRGSSLLFRRVSSGSCFALE
G.QAGLP.YSPVFKSWIHCWKYLS..GQLF.GSSLLF..VSSGS.F.LE
RetrocopyGPQAGLPRYSPVFKSWIHCWKYLSM*GQLFQGSSLLFHWVSSGSPFTLE

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 372 .86 RPM
SRP007412_cerebellum 0 .07 RPM 155 .37 RPM
SRP007412_heart 0 .00 RPM 68 .73 RPM
SRP007412_kidney 0 .00 RPM 180 .34 RPM
SRP007412_liver 0 .03 RPM 72 .18 RPM
SRP007412_testis 0 .00 RPM 41 .63 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2490 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2490 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2490 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3671
Gorilla gorilla retro_ggor_2481
Pongo abelii retro_pabe_3011
Callithrix jacchus retro_cjac_2480

Parental genes homology:
Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001374092 retrocopies
Gorilla gorilla ENSGGOG000000039081 retrocopy
Macaca mulatta ENSMMUG000000219761 retrocopy
Nomascus leucogenys ENSNLEG000000108991 retrocopy
Pongo abelii ENSPPYG000000165572 retrocopies
Pan troglodytes ENSPTRG000000035732 retrocopies
Pan troglodytes ENSPTRG00000018115 1 retrocopy
retro_ptro_2490 ,
Tarsius syrichta ENSTSYG000000147771 retrocopy
Tursiops truncatus ENSTTRG000000019662 retrocopies



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