RetrogeneDB ID:

retro_ptro_17

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:27537231..27537786(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000038999
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSPTRG00000019003
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_17
ATGGGGAAAAAACAAAACAAGAAGAAAGTGGAGGAGGTGCTAGAAGAGGAGGAAGAGGAATATGTGGTGGAAAAAGTTCT
CGACCGTCGAGTGGTAAAGGGCAAAGTGGAGTACCTCCTAAAGTGGAAGGGATTCTCAGATGAGGACAACACATGGGAGC
CAGAAGAGAACCTGGATTGCCCCGACCTCATTGCTGAGTTTCTGCAGTCACAGAAAACAGCACATGAGACAGATAAATCA
GAGGGAGGCAAGCGCAAAGCTGATTCTGATTCTGAAGATAAGGGAGAGGAGAGCAAACCAAAGAAGAAGAAAGAAGAGTC
AGAAAAGCCACGAGGCTTTGCTCGAGGTTTGGAGCCGGAGCGGATTATTGGAGCTACAGACTCCAGTGGAGAGCTCATGT
TCCTGATGAAATGGAAAAACTCTGATGAGGCTGACCTGGTCCCTGCCAAGGAAGCCAATGTCAAGTGCCCACAGGTTGTC
ATATCCTTCTATGAGGAAAGGCTGACGTGGCATTCCTACCCCTCGGAGGATGATGACAAAAAAGATGACAAGAAC

ORF - retro_ptro_17 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.88 %
Parental protein coverage: 93.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGKKQNGKS-KKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNS
MGKKQN.K....V.E.E.EE.VVEKVLDRRVV.GKVEY.LKWKGF.D.DNTWEPEENLDCP.LI..FL.S
RetrocopyMGKKQNKKKVEEVLEEEEEEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQS
ParentalQKAGKEKD---GTKRKSLSDSES--DDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLMKWKD
QK...E.D...G.KRK..SDSE.....SK.KKK.....KPRGFARGL.PERIIGATDSSGELMFLMKWK.
RetrocopyQKTAHETDKSEGGKRKADSDSEDKGEESKPKKKKEESEKPRGFARGLEPERIIGATDSSGELMFLMKWKN
ParentalSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDE
SDEADLV.AKEAN.KCPQ.VI.FYEERLTWHS.P...
RetrocopySDEADLVPAKEANVKCPQVVISFYEERLTWHSYPSED

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 8 .94 RPM 30 .19 RPM
SRP007412_cerebellum 12 .91 RPM 17 .71 RPM
SRP007412_heart 4 .34 RPM 22 .38 RPM
SRP007412_kidney 5 .20 RPM 31 .98 RPM
SRP007412_liver 2 .00 RPM 21 .93 RPM
SRP007412_testis 39 .62 RPM 73 .66 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_17 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_17 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_17 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000289711 retrocopies
Callithrix jacchus ENSCJAG000000079528 retrocopies
Loxodonta africana ENSLAFG000000069073 retrocopies
Mus musculus ENSMUSG000000298361 retrocopy
Otolemur garnettii ENSOGAG000000165831 retrocopy
Ochotona princeps ENSOPRG000000117139 retrocopies
Pan troglodytes ENSPTRG000000050341 retrocopy
Pan troglodytes ENSPTRG00000019003 10 retrocopies
Pteropus vampyrus ENSPVAG000000062972 retrocopies
Rattus norvegicus ENSRNOG000000118142 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG000000167114 retrocopies



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