RetrogeneDB ID:

retro_ptro_1804

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:99813871..99814574(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RCC2
Ensembl ID:ENSPTRG00000000247
Aliases:None
Description:Regulator of chromosome condensation 2 [Source:UniProtKB/TrEMBL;Acc:K7ABL4]


Retrocopy-Parental alignment summary:






>retro_ptro_1804
AAACTTGAAGGGTCGAAGTACAATGGGCAACTTTTGATTTGAAGGGCAGTCAACTGGGACTTGACTGGTTGAAAGGAAGT
ACCTAAACAGCAAAAGCTGCTTACGGCAATCTCGGTCAGAATTTGTGAGGGGCCTCAGATATGTGGGTACCTGGTAGCGC
CCAGGTGTGGGCAGTGGTTTCTGGTTAGTGTGCTGCTCACAGCCTCCTCATCACCATAGAAGAGAAGCTGTGGAGCTGCT
GTGGACAAGAGAAGGGGCATCTGGGACATGACAACACCAAGAGAGTGGAAGCTCCCAGACTCATCAAAGGTCTTAGCCAT
GAAGTGATCCTGCCGTCAGCATGTGGGCAGAACCACACACTGACCTTGACAGAAACCAGCTCCTTGTTCACATTTGGGGA
GAACAAGATGGCATAGCTGGGCCGTGGTAACCAGACAGATGCTGTCCACACCTTGGCACAGACAAGGTATAAAGGCCAGC
CCATTACCAAAATGACCTGTGGAGTTGAATTCAGCGTGATAATGGACTGCAAAGGAAACCCCTTTTCCTTTGGGTGCCCT
GAATATGGTCAGCTGGGACACAATTGGATGGGAAGTTCATCATCCCGATGCAGCCATTAGAATATTACTGAAAACTGGTG
CTCCTGCAATTGGCTGTCTTCATCCAGAAAACAGAAGATGGACAGATTCTGCCTGTACCAAAT

ORF - retro_ptro_1804 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.67 %
Parental protein coverage: 54.8 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKLEGSKCKGQLLIFGATNWDLIGRKEVPKQQAAYRNLGQNLW-GPHRYGCLAGVR-VRTVVSGSCAAHSL
KLEGSK..GQLLI..A.NWDL.G.KEVPKQQ............GP...G.L...R.V..VVSG.CAAHSL
RetrocopyKLEGSKYNGQLLI*RAVNWDLTG*KEVPKQQKLLTAISVRICEGPQICGYLVAPR<VWAVVSG*CAAHSL
ParentalLITTEGKLWSWGRNEKGQLGHGDTKRVEAPRLIEGLSHEVIVSAACGRNHTLALTETGSVFAFGENKMGQ
LIT.E.KLWS....EKG.LGH..TKRVEAPRLI.GLSHEVI...ACG.NHTL.LTET.S.F.FGENKM..
RetrocopyLITIEEKLWSCCGQEKGHLGHDNTKRVEAPRLIKGLSHEVILPSACGQNHTLTLTETSSLFTFGENKMA*
ParentalLGLGNQTDAVPSPAQIMYNGQPITKMACGAEFSMIMDCKGNLYSFGCPEYGQLGHN-SDGKFIARAQRIE
LG.GNQTDAV...AQ..Y.GQPITKM.CG.EFS.IMDCKGN..SFGCPEYGQLGHN..DGKFI...Q..E
RetrocopyLGRGNQTDAVHTLAQTRYKGQPITKMTCGVEFSVIMDCKGNPFSFGCPEYGQLGHN<LDGKFIIPMQPLE
ParentalYDCELVPRRVAIFIEKTKDGQILPVPN
Y...LV....A.FI.KT.DGQILPVPN
RetrocopyYY*KLVLLQLAVFIQKTEDGQILPVPN

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 42 .93 RPM
SRP007412_cerebellum 0 .00 RPM 36 .67 RPM
SRP007412_heart 0 .00 RPM 11 .08 RPM
SRP007412_kidney 0 .00 RPM 37 .42 RPM
SRP007412_liver 0 .00 RPM 32 .90 RPM
SRP007412_testis 0 .00 RPM 30 .46 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1804 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1804 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1804 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2677

Parental genes homology:
Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000013961 retrocopy
Homo sapiens ENSG000001790513 retrocopies
Gorilla gorilla ENSGGOG000000152631 retrocopy
Nomascus leucogenys ENSNLEG000000077832 retrocopies
Otolemur garnettii ENSOGAG000000145441 retrocopy
Pongo abelii ENSPPYG000000258343 retrocopies
Pan troglodytes ENSPTRG00000000247 3 retrocopies
retro_ptro_1804 , retro_ptro_2072, retro_ptro_2434,
Rattus norvegicus ENSRNOG000000063271 retrocopy



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