RetrogeneDB ID:

retro_pabe_307

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:147962018..147962761(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7
Ensembl ID:ENSPPYG00000018671
Aliases:None
Description:60S ribosomal protein L7 [Source:UniProtKB/Swiss-Prot;Acc:Q5R9R4]


Retrocopy-Parental alignment summary:






>retro_pabe_307
ATAGAAGGTGTTGAAGAGAAGAAAAAGAAGGTTCCTGCCGTGCCAGAAACCCTTAAGAAAAAGCGAAGGAATTTCACAGA
GCTGAAGATCAATCACCTAAGAAAGAAGTTTGTCCAAAATATGCTTCAAAAGGCAAGGAGGAAGCTTATCTGTGAAAAAG
CGAAGCACTATCACAAGGAATATAGGCAGATGTATAGAACTGAAATTCGAATGGTGAGGATGGCAAGAAAAGCTGGCAAC
TTCTATGTACCTGCAGAACACAGATCGGTATTTGTCATCAGGATCAGGGTTATCAATGGTGTGGCCAAAAGGTCCGAAAG
GTGTTGGGGCTTCTTCGCCTTTGTCGAATCTTCAGTGGAACTTTTGTGAAGCTTAACAAGGCTTCAATTAACATGCTGAG
GATTGTAGAACCATATATTGTATGGGGGTACCCAAATCTGATGTCAGTAAATGAACTAATCTACAAGTGTGGTTATGGCA
AAATCAATAAGAAGAGAATTACTTTGACAGACAATGCTTTGATTGCTCGATCTCTTGGTAAATATGGCATCATCTGCATG
GAGGATCTGATTAATGAGAACTATACTGTTGGAAAACACTTCAAAGAAGCAAATAACTTCCTGTGGCCCTTTGAATTATC
TTCTCCAAGAGGAGGAATGAAGAAAAAGACCACCCATTTTGTAGAAGGTGGAGATGCTGGCAACAGACAGGACCAGATCA
ACAGGTTTTTTAGAAGAATGAAC

ORF - retro_pabe_307 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.75 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEGVEEKKK-VPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIR
.EGVEEKKK.VPAVPETLKKKRRNF.ELKI..LRKKF.Q.ML.KARRKLI.EKAKHYHKEYRQMYRTEIR
RetrocopyIEGVEEKKKKVPAVPETLKKKRRNFTELKINHLRKKFVQNMLQKARRKLICEKAKHYHKEYRQMYRTEIR
ParentalMARMARKAGNFYVPAEPKLAFVIRIRGINGVSP-KVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPY
M.RMARKAGNFYVPAE....FVIRIR.INGV...KVRKVL.LLRL..IF.GTFVKLNKASINMLRIVEPY
RetrocopyMVRMARKAGNFYVPAEHRSVFVIRIRVINGVAK<KVRKVLGLLRLCRIFSGTFVKLNKASINMLRIVEPY
ParentalIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLW
I.WGYPNL.SVNELIYK.GYGKINKKRI.LTDNALIARSLGKYGIICMEDLI.E.YTVGK.FKEANNFLW
RetrocopyIVWGYPNLMSVNELIYKCGYGKINKKRITLTDNALIARSLGKYGIICMEDLINENYTVGKHFKEANNFLW
ParentalPFKLSSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN
PF.LSSPRGGMKKKTTHFVEGGDAGNR.DQINR..RRMN
RetrocopyPFELSSPRGGMKKKTTHFVEGGDAGNRQDQINRFFRRMN

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 195 .23 RPM
SRP007412_cerebellum 0 .00 RPM 236 .51 RPM
SRP007412_heart 0 .00 RPM 246 .64 RPM
SRP007412_kidney 0 .03 RPM 458 .95 RPM
SRP007412_liver 0 .00 RPM 335 .15 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_307 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_307 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_307 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_415

Parental genes homology:
Parental genes homology involve 17 parental genes, and 256 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000002013922 retrocopies
Callithrix jacchus ENSCJAG000000076861 retrocopy
Equus caballus ENSECAG000000091881 retrocopy
Homo sapiens ENSG0000014760449 retrocopies
Latimeria chalumnae ENSLACG000000035711 retrocopy
Macropus eugenii ENSMEUG000000163199 retrocopies
Microcebus murinus ENSMICG000000028808 retrocopies
Macaca mulatta ENSMMUG000000051411 retrocopy
Monodelphis domestica ENSMODG000000071364 retrocopies
Otolemur garnettii ENSOGAG000000039032 retrocopies
Pongo abelii ENSPPYG0000001661921 retrocopies
Pongo abelii ENSPPYG00000018671 50 retrocopies
Rattus norvegicus ENSRNOG0000000699227 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000458618 retrocopies
Tupaia belangeri ENSTBEG000000023011 retrocopy
Tarsius syrichta ENSTSYG0000000610025 retrocopies
Tursiops truncatus ENSTTRG0000000907416 retrocopies



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