RetrogeneDB ID:

retro_ptro_365

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:163789983..163790308(-)
Located in intron of:ENSPTRG00000001777
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22
Ensembl ID:ENSPTRG00000000076
Aliases:None
Description:ribosomal protein L22 [Source:HGNC Symbol;Acc:10315]


Retrocopy-Parental alignment summary:






>retro_ptro_365
AAGCAGGTTCTGAAGTTCACTCTTGATTGCACCCACCCCATAGAAGATGGATCATGGATGCTGCCAATTTTGAGCAGTTT
TTGCAAGAGGATCAAAGTGAGCAGAAAAGCTAGGAATGTCATTGGAGGGGTTGTGATCAAAAGGAGCAAGGGCAAGATCA
CCATGACTTCCGAGATGCCTCTTCCCAAAAGGTATTTGAAATAAGAAATATTTGAAGAAGAACAATCTACGTGATTGGAC
GTGCGTAACTGCTAACAGCAAAAGGGGTTATGAATTACGTTACTTCCAAATTAACCAGAACAAACAAGAGGAGGAAGACG
AGGAT

ORF - retro_ptro_365 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.79 %
Parental protein coverage: 88.28 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSKITVTSEVPFSKRYLKY
KQVLKFTLDCTHP.EDG.........F...RIKV..KA.N..GGVV.I.RSK.KIT.TSE.P..K....Y
RetrocopyKQVLKFTLDCTHPIEDGSWMLPILSSFCK-RIKVSRKARNVIGGVV-IKRSKGKITMTSEMPLPK---RY
ParentalL-TKKYLKKNNLRDWLRVVANSKESYELRYFQINQDEEEEEDED
L..KKYLKKNNLRDW..V.ANSK..YELRYFQINQ...EEEDED
RetrocopyL>NKKYLKKNNLRDWTCVTANSKRGYELRYFQINQNKQEEEDED

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 .13 RPM 120 .78 RPM
SRP007412_cerebellum 0 .36 RPM 300 .48 RPM
SRP007412_heart 0 .20 RPM 196 .18 RPM
SRP007412_kidney 0 .26 RPM 266 .30 RPM
SRP007412_liver 0 .20 RPM 228 .58 RPM
SRP007412_testis 0 .21 RPM 173 .25 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_365 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_365 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_365 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_485
Pongo abelii retro_pabe_248
Macaca mulatta retro_mmul_445

Parental genes homology:
Parental genes homology involve 21 parental genes, and 183 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098647 retrocopies
Bos taurus ENSBTAG000000144234 retrocopies
Choloepus hoffmanni ENSCHOG000000074772 retrocopies
Callithrix jacchus ENSCJAG0000000013212 retrocopies
Dasypus novemcinctus ENSDNOG000000131668 retrocopies
Felis catus ENSFCAG000000063203 retrocopies
Homo sapiens ENSG0000011625116 retrocopies
Gorilla gorilla ENSGGOG0000002773910 retrocopies
Loxodonta africana ENSLAFG000000063525 retrocopies
Macaca mulatta ENSMMUG0000001834712 retrocopies
Mustela putorius furoENSMPUG000000070876 retrocopies
Mus musculus ENSMUSG000000289365 retrocopies
Nomascus leucogenys ENSNLEG0000001033710 retrocopies
Otolemur garnettii ENSOGAG000000147767 retrocopies
Pongo abelii ENSPPYG0000000195111 retrocopies
Pan troglodytes ENSPTRG00000000076 14 retrocopies
Rattus norvegicus ENSRNOG000000111045 retrocopies
Sus scrofa ENSSSCG000000033674 retrocopies
Tupaia belangeri ENSTBEG0000000917233 retrocopies
Tursiops truncatus ENSTTRG000000104888 retrocopies
Vicugna pacos ENSVPAG000000094661 retrocopy



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