RetrogeneDB ID:

retro_ptro_407

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:10:8720398..8721076(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CHCHD3
Ensembl ID:ENSPTRG00000019711
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_407
GGTGGGACCTTGAGCACTCATCGGGTCACCTTCGAGGTGGACAAGAATGAGAACATCACCCATCACTGTGGTGAAGGGCA
TTGAGCTTTCAGAAAATGTGATTGATTGAATGAAGGAATCCTCTCCATCTGGTTCAAAGTCTCAGTGGTATTCTGATGCT
TATGATGCCTTGGTTTCTGATGAAGAATTGAAAAGAAGAGTAGCTGAGGAGCTAACATTGGAACAAGCCAAGAAACAAAC
TGAAGATCAGAAACGACTAAAGCAAGCCACAGAGCTGGAGAGAGAGAGGGCTGCTGCCAATGGGCAGTTAACCAGAGCCA
TCCCTCGAGAGAAGGTATCAAGCCAGGAGGAAGGCACTAAGGCAATGCACCTGGCTAGGTGGCTGGAAGAGAAAGGCCGA
GTGCTAAAGAAGCAGGTTGCATTCTGCAAAGTGGAGCTGGCTAGACTGGAGGAGAGGAGCTCAGAGTTCTACAAAGTCAC
CACTGAACAATATCAGAAAATTGCTGAAGAGGTGGAAGCACGGTTCAAGTGTATGAGTCTCATCCAGTCTATGCTGACCT
CCAGGCCAAAATTCTTCAGTGTTACTACGAGAACACCCACCAGACCTTCAAATGCTCCACTCTGGCCAGCCGGTATATGC
CCTATGTCAATCATGCCAAACAGAGCATGCTTGAGAAA

ORF - retro_ptro_407 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.39 %
Parental protein coverage: 98.68 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGGTTSTRRVTFEA--DEN-ENITVVKGIRLSENVIDRMKESSPSGSKSQRYSGAYGASVSDEELKRRVAE
GGT.ST.RVTFE....EN...ITVVKGI.LSENVID.MKESSPSGSKSQ.YS.AY.A.VSDEELKRRVAE
RetrocopyGGTLSTHRVTFEVDKNEN>SPITVVKGIELSENVID*MKESSPSGSKSQWYSDAYDALVSDEELKRRVAE
ParentalELALEQAKKESEDQKRLKQAKELDRERAAANEQLTRAILRERISSEEERAKAKHLARQLEEKDRVLKKQD
EL.LEQAKK..EDQKRLKQA.EL.RERAAAN.QLTRAI.RE..SS.EE..KA.HLAR.LEEK.RVLKKQ.
RetrocopyELTLEQAKKQTEDQKRLKQATELERERAAANGQLTRAIPREKVSSQEEGTKAMHLARWLEEKGRVLKKQV
ParentalAFYKEQLARLEERSSEFYRVTTEQYQKAAEEVEAKFK-RYESHPVCADLQAKILQCYRENTHQTLKCSAL
AF.K..LARLEERSSEFY.VTTEQYQK.AEEVEA.FK..YESHPV.ADLQAKILQCY.ENTHQT.KCS.L
RetrocopyAFCKVELARLEERSSEFYKVTTEQYQKIAEEVEARFK<VYESHPVYADLQAKILQCYYENTHQTFKCSTL
ParentalATQYMHCVNHAKQSMLEK
A..YM..VNHAKQSMLEK
RetrocopyASRYMPYVNHAKQSMLEK

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 16 .14 RPM
SRP007412_cerebellum 0 .00 RPM 13 .19 RPM
SRP007412_heart 0 .00 RPM 62 .43 RPM
SRP007412_kidney 0 .00 RPM 38 .42 RPM
SRP007412_liver 0 .00 RPM 25 .14 RPM
SRP007412_testis 0 .00 RPM 13 .59 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_407 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_407 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_407 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_542
Pongo abelii retro_pabe_501

Parental genes homology:
Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000013121 retrocopy
Dasypus novemcinctus ENSDNOG000000049421 retrocopy
Homo sapiens ENSG000001065543 retrocopies
Macaca mulatta ENSMMUG000000016711 retrocopy
Mus musculus ENSMUSG000000537681 retrocopy
Nomascus leucogenys ENSNLEG000000129673 retrocopies
Oryctolagus cuniculus ENSOCUG000000140321 retrocopy
Pongo abelii ENSPPYG000000258275 retrocopies
Pan troglodytes ENSPTRG00000019711 4 retrocopies
Rattus norvegicus ENSRNOG000000132111 retrocopy
Sorex araneus ENSSARG000000121111 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000222821 retrocopy



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