RetrogeneDB ID:

retro_pabe_2262

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:141276007..141276840(+)
Located in intron of:ENSPPYG00000014147
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSPPYG00000004189
Aliases:GAPDH, GAPD
Description:glyceraldehyde-3-phosphate dehydrogenase [Source:RefSeq peptide;Acc:NP_001125767]


Retrocopy-Parental alignment summary:






>retro_pabe_2262
GTAAACTGATTTGGCCTTATTAGACACCTGGTCACCAAGGCTGCTTTTAACTCTGGTGAAGTGGATATTGTCTACATCAA
GGACCCCCTCATTGTCCTCAACTACACAGTCTATATGTTCCATGATGATTCTACCCATGGCAAGTTTCGTGGCACAGTCA
AGGCTGAGAATGGCAAGCTTGTCATCAGTGAAAATACCATAACCATTTTCTAGGAGCAAATTCCCACCAAAATCAAATTG
GGTGATGCCACCACAATTACACTGTGGAGACCACTGGCATCTTCACTACCTTGTAGAAGGCTGGGGCTCATTTAAAAGGA
GGAACTGAAAGGGTCATCATCTCTGTCCCCTCTGCTGATGCCCCCATGTTTGTGATGGGCATGAACCATGAAAAGTACAA
AAACACCTCGCAATTCCCAGCAAACCTTCTATACCACTAACTGCTTAGCACCACTGGCCAAGATCACCCATGACAACTTT
GGCATTGTGGGAGGAATCATGACCTCGTCCATGCTACTATCACTGACATCCAGAAGACCACTGATGGCCCATCTGGGAAA
CTGTGGTGCGATGGCCACAGGGCTTTCCAGAACATCACTCCTGTACCTATTGGTGCTGCCAAAGCTGTGGGCAAAGTCAT
CTCCAAGCTGAGCAGGGAGCTCACTGGCATAGCCTTCTATGTCCCCACAGGCAATGTGTCCGTCATGGACCTGACCTACC
ATCTGGAAAGACCTGCCAAATACAACGACATCACGAAGGAGGTGAAGCAGGAGTGGAAGGGCCCCCTCAAAGGCATCCTG
GGCTACTCTGAGTACCAGGTTGTCTCTGCCAAC

ORF - retro_pabe_2262 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.26 %
Parental protein coverage: 82.99 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalINGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGNPITIF
.N.FG.I..LVT.AAFNSG.VDIV.I.DP.I.LNY.VYMF..DSTHGKF.GTVKAENGKLVI..N.ITIF
RetrocopyVN*FGLIRHLVTKAAFNSGEVDIVYIKDPLIVLNYTVYMFHDDSTHGKFRGTVKAENGKLVISENTITIF
ParentalQERDPSKIKWGDAGA-EYVVESTGVFTTMEKAGAHLQGGAKRVIISAPSADAPMFVMGVNHEKYDNS-LK
.E..P.KIK.GDA....Y.VE.TG.FTT..KAGAHL.GG..RVIIS.PSADAPMFVMG.NHEKY.N..L.
Retrocopy*EQIPTKIKLGDATT<NYTVETTGIFTTL*KAGAHLKGGTERVIISVPSADAPMFVMGMNHEKYKNT<LA
ParentalIVSNASC-TTNCLAPLAKVIHDNFGIVEGLMTT-VHA-ITATQKTVDGPSGKLWRDGRGALQNIIPASTG
I.S..S..TTNCLAPLAK..HDNFGIV.G.MT..VHA.IT..QKT.DGPSGKLW.DG..A.QNI.P...G
RetrocopyIPSKPSI<TTNCLAPLAKITHDNFGIVGGIMTS<VHATITDIQKTTDGPSGKLWCDGHRAFQNITPVPIG
ParentalAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILGYTEHQVV
AAKAVGKVI..L...LTG.AF.VPT.NVSV.DLT..LE..AKY.DI.K.VKQ...GPLKGILGY.E.QVV
RetrocopyAAKAVGKVISKLSRELTGIAFYVPTGNVSVMDLTYHLERPAKYNDITKEVKQEWKGPLKGILGYSEYQVV
ParentalSSD
S..
RetrocopySAN

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 .06 RPM 1579 .43 RPM
SRP007412_cerebellum 0 .00 RPM 972 .32 RPM
SRP007412_heart 0 .18 RPM 1118 .01 RPM
SRP007412_kidney 0 .13 RPM 892 .74 RPM
SRP007412_liver 0 .09 RPM 668 .25 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2262 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2262 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2262 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2711
Pan troglodytes retro_ptro_1832
Gorilla gorilla retro_ggor_1889
Macaca mulatta retro_mmul_1535

Parental genes homology:
Parental genes homology involve 20 parental genes, and 509 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Canis familiaris ENSCAFG000000150774 retrocopies
Cavia porcellus ENSCPOG000000263501 retrocopy
Erinaceus europaeus ENSEEUG000000114443 retrocopies
Homo sapiens ENSG0000011164042 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG000000027803 retrocopies
Macropus eugenii ENSMEUG0000001527367 retrocopies
Microcebus murinus ENSMICG0000000654616 retrocopies
Macaca mulatta ENSMMUG0000001867933 retrocopies
Monodelphis domestica ENSMODG0000001806641 retrocopies
Mustela putorius furoENSMPUG0000001689128 retrocopies
Mus musculus ENSMUSG00000057666109 retrocopies
retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Pongo abelii ENSPPYG00000004189 38 retrocopies
Pan troglodytes ENSPTRG0000000457743 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



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