RetrogeneDB ID:

retro_pabe_2506

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:17252905..17253470(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000025872
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_2506
AGCGCCAAGATCGTGAAGCCCAGCTGCGGGAAGCTGAGTATGTTCGAGTGTAGCTCTTCCAGGCACTTCTGAAGCTGGAG
ATGAACTTGGACCTCAGGCTCAGCTCAGGGAGCTGAAAATTATGGCAGCCAAGGAAATTGAAGTTGGTGGTGGTCAGAAA
GCTATCATCATCTTTGTTCCTGTTCCTCAACTGAATCTTTCCAGAAAATCCACATCTGGCTAGTACATGAATTGGAGAAA
AAGTTCAGTGGGGAAGAATGTTGTTTTCATTGTTCAGAGGAGAATTCTGCCTAAGGCAACTCAAAAAAGCCATACAAACA
ATAAGCAAAAGTGTCCCAGGAGCCGTACTCTGACAGCCATGCATGGTACCATCCTTGAGGACTTGCTTTTCCCAAGTGAA
ATTATGCACGAGAGAATATGCATGAAACTGGATGGCAGCCGGCTGATGAAAGTTCATTCAGACAAAGCACAGCAGAACAA
TGTGGAACACGGGGTTGAGACTTTTTCTGATGTCTATAAGAAGCTCACTGGCAAGGATGTTAATTTTGAATTCCAAGAGT
TTCAG

ORF - retro_pabe_2506 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.68 %
Parental protein coverage: 97.42 %
Number of stop codons detected: 0
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalSAKIVKPNGEKPDEFESGIS-QALLELEMNSDLK-AQLRELNITAAKEIEVGGGRKAIIIFVPVPQL-KS
SAKIVKP...K...FE...S.QALL.LEMN.DL..AQLREL.I.AAKEIEVGGG.KAIIIFVPVPQL..S
RetrocopySAKIVKPSCGKLSMFECSSS<QALLKLEMNLDLR<AQLRELKIMAAKEIEVGGGQKAIIIFVPVPQL<ES
ParentalFQKIQVRLVRELEKKFSG-KHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIV
FQKI...LV.ELEKKFSG.K.VVFI.QRRILPK.T.KS.T.NKQK.PRSRTLTA.H..ILEDL.FPSEI.
RetrocopyFQKIHIWLVHELEKKFSG>KNVVFIVQRRILPKATQKSHTNNKQKCPRSRTLTAMHGTILEDLLFPSEIM
ParentalGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQ
..RI..KLDGSRL.KVH.DKAQQNNVEH.VETFS.VYKKLTGKDVNFEF.EFQ
RetrocopyHERICMKLDGSRLMKVHSDKAQQNNVEHGVETFSDVYKKLTGKDVNFEFQEFQ

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 28 .03 RPM
SRP007412_cerebellum 0 .00 RPM 39 .52 RPM
SRP007412_heart 0 .00 RPM 36 .49 RPM
SRP007412_kidney 0 .00 RPM 59 .47 RPM
SRP007412_liver 0 .00 RPM 62 .52 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2506 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2506 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2506 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2090

Parental genes homology:
Parental genes homology involve 23 parental genes, and 120 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000162245 retrocopies
Canis familiaris ENSCAFG000000032631 retrocopy
Callithrix jacchus ENSCJAG000000164622 retrocopies
Cavia porcellus ENSCPOG000000097952 retrocopies
Dasypus novemcinctus ENSDNOG0000001328514 retrocopies
Equus caballus ENSECAG000000202532 retrocopies
Felis catus ENSFCAG000000232432 retrocopies
Homo sapiens ENSG0000017186314 retrocopies
Gorilla gorilla ENSGGOG0000002309513 retrocopies
Loxodonta africana ENSLAFG0000001508711 retrocopies
Myotis lucifugus ENSMLUG000000061211 retrocopy
Monodelphis domestica ENSMODG000000144952 retrocopies
Mus musculus ENSMUSG000000614772 retrocopies
Nomascus leucogenys ENSNLEG0000001540710 retrocopies
Oryctolagus cuniculus ENSOCUG000000085072 retrocopies
Otolemur garnettii ENSOGAG000000281651 retrocopy
Ochotona princeps ENSOPRG000000050853 retrocopies
Pongo abelii ENSPPYG00000025872 12 retrocopies
Pan troglodytes ENSPTRG000000116153 retrocopies
Pteropus vampyrus ENSPVAG000000020717 retrocopies
Rattus norvegicus ENSRNOG000000085512 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000248303 retrocopies
Tursiops truncatus ENSTTRG000000016166 retrocopies



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