RetrogeneDB ID:

retro_ptro_2229

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:17726019..17726427(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3C
Ensembl ID:ENSPTRG00000002045
Aliases:None
Description:Pan troglodytes histone cluster 1, H3a (HIST1H3A), mRNA. [Source:RefSeq mRNA;Acc:NM_001098568]


Retrocopy-Parental alignment summary:






>retro_ptro_2229
ATGGCAGGCACCAAGCAGACCGCCCGCAAAGCCACCGCCTGGCAGGCCCCCAGGAAGCCCCTGGCCACCAAAGCCGCCAG
AAAAAGGGCGCCGCCTACAGGAGGGATCAAGAAGCCTCACCGCTACAAGCCTGGCACCCTGGCGCTGCGGGAAATCAGAA
AGTACCAGAAGTCCACGCAGCTGCTCCTGCGCAAGCTGCCCTTCCAGCGCCTGGTGCGCGAGATCGCCCAGGCCATCAGG
CCGGACCTGCGCTTCCAGAGCGCGGCCATTGGCGCCCTGCAGGAGGCCAGCGAGGCCTACCTGGTGCAACTCTTTGAAGA
CACCAACTTGCGTGCCATCCGTGCCAGGCGCGTCACAATTATGCCCCAAGACATGCAGCTGGCCCGCCGCCTCCGTGGAG
AGGGTGCC

ORF - retro_ptro_2229 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.88 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
MA.TKQTARK.T...APRK.LATKAARK.AP.TGG.KKPHRY.PGT.ALREIR.YQKST.LL.RKLPFQR
RetrocopyMAGTKQTARKATAWQAPRKPLATKAARKRAPPTGGIKKPHRYKPGTLALREIRKYQKSTQLLLRKLPFQR
ParentalLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
LVREIAQ....DLRFQSAAIGALQEASEAYLV.LFEDTNL.AI.A.RVTIMP.D.QLARR.RGE.A
RetrocopyLVREIAQAIRPDLRFQSAAIGALQEASEAYLVQLFEDTNLRAIRARRVTIMPQDMQLARRLRGEGA

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 5 .72 RPM
SRP007412_cerebellum 0 .00 RPM 0 .50 RPM
SRP007412_heart 0 .00 RPM 0 .61 RPM
SRP007412_kidney 0 .00 RPM 1 .10 RPM
SRP007412_liver 0 .00 RPM 0 .69 RPM
SRP007412_testis 0 .11 RPM 1 .79 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2229 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2229 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2229 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 111 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000145887 retrocopies
Bos taurus ENSBTAG000000245613 retrocopies
Canis familiaris ENSCAFG000000049162 retrocopies
Canis familiaris ENSCAFG000000161194 retrocopies
Erinaceus europaeus ENSEEUG000000137961 retrocopy
Felis catus ENSFCAG000000036174 retrocopies
Felis catus ENSFCAG000000304245 retrocopies
Gadus morhua ENSGMOG000000143061 retrocopy
Macaca mulatta ENSMMUG000000314839 retrocopies
Monodelphis domestica ENSMODG000000059833 retrocopies
Mustela putorius furoENSMPUG000000138113 retrocopies
Nomascus leucogenys ENSNLEG000000015772 retrocopies
Otolemur garnettii ENSOGAG0000002431211 retrocopies
Otolemur garnettii ENSOGAG0000002593314 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Pan troglodytes ENSPTRG00000002045 20 retrocopies
Pan troglodytes ENSPTRG0000000965512 retrocopies
Pteropus vampyrus ENSPVAG000000084592 retrocopies
Tursiops truncatus ENSTTRG000000158897 retrocopies



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