RetrogeneDB ID:

retro_ptro_2235

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:18838145..18838452(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFA5
Ensembl ID:ENSPTRG00000019637
Aliases:None
Description:Pan troglodytes NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa (NDUFA5), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071797]


Retrocopy-Parental alignment summary:






>retro_ptro_2235
TTGGCTTTATGAAAGAGCCTACATGAGAGGCTAAGAATATTGTACACAAAGACTCTTGATATTCTTTAGCAAATCCCTAA
AAATGAAGCATATAAAAAGCATACAGAACAGATTACAAATGACAAGCTGGCTATGGCTGAAGTGGAACCAGATGTTAAAG
AACTAGAAGACCAACTTCAAGGTGGCCCAATAGAAGAGCGATTCTTCAGGCTGCAAATGAACAAAGTCTGGCAAGAAAAA
TAATGCAGTGGAAATTATGGGAACCATTAGTATAAGAGTTCCCACCAATCAGTGGGAATGACCAATA

ORF - retro_ptro_2235 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.67 %
Parental protein coverage: 88.79 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLAVCNTPHERLRILYTKILDVLEEIPKNAAYRKYTEQITNEKLAMVKAEPDVKKLEDQLQGGQLEE-VIL
LA.....HERLRILYTK.LD.L..IPKN.AY.K.TEQITN.KLAM...EPDVK.LEDQLQGG..EE..IL
RetrocopyLAL*KSLHERLRILYTKTLDIL*QIPKNEAYKKHTEQITNDKLAMAEVEPDVKELEDQLQGGPIEE<AIL
ParentalQAEHELNLARKMREWKLWEPLVEE-PPADQWKWPI
QA..E..LARK...WKLWEPLV.E..P..QW..PI
RetrocopyQAANEQSLARKIMQWKLWEPLV*E<VPTNQWE*PI

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 37 .93 RPM
SRP007412_cerebellum 0 .00 RPM 25 .74 RPM
SRP007412_heart 0 .00 RPM 72 .17 RPM
SRP007412_kidney 0 .00 RPM 33 .79 RPM
SRP007412_liver 0 .00 RPM 13 .98 RPM
SRP007412_testis 0 .00 RPM 15 .81 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2235 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2235 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2235 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3218
Gorilla gorilla retro_ggor_2185
Pongo abelii retro_pabe_2666

Parental genes homology:
Parental genes homology involve 17 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000045122 retrocopies
Bos taurus ENSBTAG000000093345 retrocopies
Canis familiaris ENSCAFG000000251124 retrocopies
Callithrix jacchus ENSCJAG000000174491 retrocopy
Felis catus ENSFCAG000000271255 retrocopies
Homo sapiens ENSG0000012860910 retrocopies
Gorilla gorilla ENSGGOG000000229229 retrocopies
Loxodonta africana ENSLAFG000000309711 retrocopy
Monodelphis domestica ENSMODG000000153844 retrocopies
Mustela putorius furoENSMPUG000000068114 retrocopies
Mus musculus ENSMUSG000000230892 retrocopies
Otolemur garnettii ENSOGAG000000331376 retrocopies
Pongo abelii ENSPPYG0000001795610 retrocopies
Pan troglodytes ENSPTRG00000019637 10 retrocopies
Rattus norvegicus ENSRNOG000000056983 retrocopies
Sus scrofa ENSSSCG000000166072 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000274041 retrocopy



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