RetrogeneDB ID:

retro_pabe_2238

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:106131734..106132621(+)
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:ENSPPYG00000001152
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_2238
GGGTTTGCTAAAGTTGTCAGAAACAAGGCCTGCTTTAAGAGAAACCAAGTGAAATTCAGAAAATGATAGGAGGATAAAAA
CCGAAGATTATACTTGGAAACGCTTGGTGATACTGTATAAAAATAAGTACAACACACCCAAATACAGGATGATAGTTTGG
TGACAAACAGAGACATCATTTGTCAGACTGCTTATGCCTGTATAGGAGGGGATATGATAGTCTGCACAGCTTAAGCATAT
AAACTGCCAAAATATGGTGTGAAGGTTGGCCTGACACATTATGCTACAGCATATTGTACTGGCTTGCTGCTGGCCCACAG
GCTTCTCAGTAAGTCTGGCATGGACAAGATTTATGAAGGCCAAGTGGAGGTGACCAGAGATGAATACAACGTGGAAAACA
TTGATGGTCAGCTGGGTGTTTTTACCTGCTATTTGAAGGCAGGCCTTGCCAGAACCACCACTAGTAATAAAGTTTTGGGG
GCCCTGAAGGGGGCTGTGAATGGAGGCCTCTCTATCTCTCACAGTAACAGATTCCCTGCTTATGATTCTGAAAGCAAGGC
ATTTAATGCGAAAGTACATAGGAAGCATATCATGGGTCAGAATGTTACAGATTACATGCATTACCTAATGGAAGAAGCTG
AAGATCTTACAAGAAACAGTTTTCTCAATACATAAAGAACAGCATAACTCCATACATGATGGAGGAGATGTATAAGAAAG
CCTACATTGCTATATGAGAGAACCCAGGCTATGAGAAGAAGCCCAAGAAAGAAGCTAAAGAGAAAATATTTCCACCTCAT
CCCAAAACGTCTCTTGCCCAGAAGAAACACTGGGTAGTTCAAAAGAAGGCAAGCTTCATCAGAGCTGGAGAACAGGCTGC
TGAGAGC

ORF - retro_pabe_2238 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77. %
Parental protein coverage: 99.66 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGFVKVVKNKAYFKRYQVKFRR-RREGKTDYYARKRLVIQDKNKYNTPKYRMIV-RVTNRDIICQIAYARI
GF.KVV.NKA.FKR.QVKFR...R..KT..Y..KRLVI..KNKYNTPKYRMIV..VTNRDIICQ.AYA.I
RetrocopyGFAKVVRNKACFKRNQVKFRK>DRRIKTEDYTWKRLVILYKNKYNTPKYRMIV<LVTNRDIICQTAYACI
ParentalEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQP
.GDMIVC.A.A..LPKYGVKVGLT.YA.AYCTGLLLA.RLL...GMDKIYEGQVEVT.DEYNVE.IDGQ.
RetrocopyGGDMIVCTA*AYKLPKYGVKVGLTHYATAYCTGLLLAHRLLSKSGMDKIYEGQVEVTRDEYNVENIDGQL
ParentalGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYMR
G.FTCYL.AGLARTTT.NKV.GALKGAV.GGLSI.HS..RFP.YDSESK.FNA.VHRKHIMGQNV.DYM.
RetrocopyGVFTCYLKAGLARTTTSNKVLGALKGAVNGGLSISHS-NRFPAYDSESKAFNAKVHRKHIMGQNVTDYMH
ParentalYLMEEDED-AYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPKKEVKKKRW-NRPKMSLAQKK
YLMEE.ED..YKKQFSQYIKNS.TP.MMEEMYKKA..AI.ENP.YEKKPKKE.K.K.....PK.SLAQKK
RetrocopyYLMEEAED<SYKKQFSQYIKNSITPYMMEEMYKKAYIAI*ENPGYEKKPKKEAKEKIFPPHPKTSLAQKK
ParentalDRVAQKKASFLRAQERAAES
..V.QKKASF.RA.E.AAES
RetrocopyHWVVQKKASFIRAGEQAAES

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 43 .02 RPM
SRP007412_cerebellum 0 .00 RPM 43 .29 RPM
SRP007412_heart 0 .00 RPM 58 .73 RPM
SRP007412_kidney 0 .00 RPM 101 .00 RPM
SRP007412_liver 0 .00 RPM 85 .29 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2238 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2238 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2238 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2777
Pan troglodytes retro_ptro_1878
Gorilla gorilla retro_ggor_1934

Parental genes homology:
Parental genes homology involve 19 parental genes, and 166 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000201504 retrocopies
Erinaceus europaeus ENSEEUG000000028521 retrocopy
Echinops telfairi ENSETEG000000098898 retrocopies
Felis catus ENSFCAG000000246805 retrocopies
Homo sapiens ENSG0000012240630 retrocopies
Gorilla gorilla ENSGGOG0000000269924 retrocopies
Loxodonta africana ENSLAFG000000119166 retrocopies
Macropus eugenii ENSMEUG000000063613 retrocopies
Myotis lucifugus ENSMLUG000000089561 retrocopy
Monodelphis domestica ENSMODG000000116351 retrocopy
Nomascus leucogenys ENSNLEG000000105002 retrocopies
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
Otolemur garnettii ENSOGAG000000132466 retrocopies
Procavia capensis ENSPCAG000000118652 retrocopies
Petromyzon marinus ENSPMAG000000020401 retrocopy
Pongo abelii ENSPPYG00000001152 32 retrocopies
Pan troglodytes ENSPTRG0000000096330 retrocopies
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
Tarsius syrichta ENSTSYG000000140388 retrocopies



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