RetrogeneDB ID:

retro_pabe_2434

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:51223858..51224452(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:APOO
Ensembl ID:ENSPPYG00000020191
Aliases:None
Description:apolipoprotein O [Source:HGNC Symbol;Acc:28727]


Retrocopy-Parental alignment summary:






>retro_pabe_2434
ATGTTCAAGGTAATTCGGAGGTCCGTGAGGCCAACCAGCCTACACTTGTTCACCTTCAAAGTCTATGCAGCACCAAAAAA
GGACTCACCTTCCCAAAATCCCGTGAAGGTTGATGAGCTTTCACTGTACTCAGTTCCCGAGGGTCAATCGAAGTGTGTGG
AAGAGTCAAGGAGCCAGCTTGAAGAAGGCATCTCACAGTTCCGACGCTATTGTGAGCCACATAGAAATTTGTGTCAGGAA
ACTTACTCCCAAACCAAGCCTAAGATGCAAAGTTTGGTTCAGTGGGGGTTAGACAGCTATGAATATCTCCAAAATGCACC
TCCTGGATTTTTTCCCAGACTTGGTGTTATTGGTTTTGCTAGCCTTAATGGACTCTTTCTGGCTAGAGGTTCAAAAATAA
AGAAGCTAGTGTGTCCACCTGGTTTCATGGGATTAGCTGCCTCCATCTGTTATCCACAACAAGCTATCGTGTTTGCCAAG
GTCAGTGGGGAGAGATTACATGACTGGGGTTTACACGGATATATAGTAATGGAAGATTTGTGGAAGGAGAACTTTTAAAA
GCCAGGAAATGTGAAAAATTCACCTGGAGCAGAG

ORF - retro_pabe_2434 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.34 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFKVIQRSVGPASLSLLTFKVYAAPKKDSPPKNSVKVDELSLYSVPEGQSKYVEEARSQLEESISQLRHY
MFKVI.RSV.P.SL.L.TFKVYAAPKKDSP..N.VKVDELSLYSVPEGQSK.VEE.RSQLEE.ISQ.R.Y
RetrocopyMFKVIRRSVRPTSLHLFTFKVYAAPKKDSPSQNPVKVDELSLYSVPEGQSKCVEESRSQLEEGISQFRRY
ParentalCEPYTTWCQETYSQTKPKMQSLVQWGLDSYDYLQNAPPGFFPRLGVIGFAGLIGLLLARGSKIKKLVYPP
CEP....CQETYSQTKPKMQSLVQWGLDSY.YLQNAPPGFFPRLGVIGFA.L.GL.LARGSKIKKLV.PP
RetrocopyCEPHRNLCQETYSQTKPKMQSLVQWGLDSYEYLQNAPPGFFPRLGVIGFASLNGLFLARGSKIKKLVCPP
ParentalGFMGLAASLYYPQQAIVFAQVSGERLYDWGLRGYIVIEDLWKENFQKPGNVKNSPGTK
GFMGLAAS..YPQQAIVFA.VSGERL.DWGL.GYIV.EDLWKENF.KPGNVKNSPG..
RetrocopyGFMGLAASICYPQQAIVFAKVSGERLHDWGLHGYIVMEDLWKENF*KPGNVKNSPGAE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 15 .15 RPM
SRP007412_cerebellum 0 .00 RPM 13 .01 RPM
SRP007412_heart 0 .00 RPM 15 .44 RPM
SRP007412_kidney 0 .00 RPM 13 .89 RPM
SRP007412_liver 0 .00 RPM 3 .43 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_2434 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2434 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2434 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3047
Pan troglodytes retro_ptro_1992
Parental genes homology:
Parental genes homology involve 23 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000127491 retrocopy
retro_amel_1282,
Choloepus hoffmanni ENSCHOG000000002262 retrocopies
retro_chof_2372, retro_chof_839,
Callithrix jacchus ENSCJAG000000049098 retrocopies
retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792, retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Dasypus novemcinctus ENSDNOG000000067101 retrocopy
retro_dnov_2450,
Equus caballus ENSECAG000000134411 retrocopy
retro_ecab_145,
Echinops telfairi ENSETEG000000141503 retrocopies
retro_etel_1052, retro_etel_516, retro_etel_711,
Felis catus ENSFCAG000000000293 retrocopies
retro_fcat_1203, retro_fcat_1657, retro_fcat_1798,
Homo sapiens ENSG000001848315 retrocopies
retro_hsap_1018, retro_hsap_1693, retro_hsap_2670, retro_hsap_3047, retro_hsap_3259,
Gorilla gorilla ENSGGOG000000012004 retrocopies
retro_ggor_1269, retro_ggor_1863, retro_ggor_2098, retro_ggor_806,
Loxodonta africana ENSLAFG000000290701 retrocopy
retro_lafr_1114,
Macropus eugenii ENSMEUG000000142221 retrocopy
retro_meug_700,
Macaca mulatta ENSMMUG000000163614 retrocopies
retro_mmul_1584, retro_mmul_1886, retro_mmul_2051, retro_mmul_814,
Monodelphis domestica ENSMODG000000255541 retrocopy
retro_mdom_1510,
Mustela putorius furoENSMPUG000000001091 retrocopy
retro_mputfur_109,
Mus musculus ENSMUSG000000795081 retrocopy
retro_mmus_282,
Nomascus leucogenys ENSNLEG000000100265 retrocopies
retro_nleu_1167, retro_nleu_1338, retro_nleu_1944, retro_nleu_456, retro_nleu_898,
Pongo abelii ENSPPYG00000020191 7 retrocopies
retro_pabe_1394, retro_pabe_1417, retro_pabe_2215, retro_pabe_2417, retro_pabe_2434 , retro_pabe_2702, retro_pabe_856,
Pongo abelii ENSPPYG000000205161 retrocopy
retro_pabe_2697,
Pan troglodytes ENSPTRG000000217425 retrocopies
retro_ptro_1147, retro_ptro_1799, retro_ptro_1992, retro_ptro_2205, retro_ptro_746,
Pteropus vampyrus ENSPVAG000000025302 retrocopies
retro_pvam_128, retro_pvam_594,
Sarcophilus harrisii ENSSHAG000000087341 retrocopy
retro_shar_125,
Sus scrofa ENSSSCG000000121741 retrocopy
retro_sscr_774,
Tarsius syrichta ENSTSYG000000102392 retrocopies
retro_tsyr_1089, retro_tsyr_2155,


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