RetrogeneDB ID:

retro_pabe_1779

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:20:8151913..8152708(+)
Located in intron of:ENSPPYG00000010714
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_1779
AAGGTGAAGGCCCAAGTAAAAGGATTTGGCAGTACTGGGCGCTGGTCACCAGGGCTGCTTTTGACTCTGGTAAAGTAGTG
TTCTCGCCATCAATGACCCTTCCCTTGACCTCAACTACATAGTCTACATGTTCCCATATGATTCCACCCACAGCAAATCC
CACGGCACCATCAAGGCTGAGAATGGGAAGCTTGTCATCAATGGAAATCCCATCAGCATCTTCTAGGAGTGAGATCCCAC
CAAAATCAAATGGGGCCATGCTGGTGCTGAGTACATTATGGAGTCCACCAGTATCTTCACGACCATGGAGAAGGCTGGAG
CTCACTTGCAGCAGGGAGCCAAAAGGGTCATCATCTCTGCTCTCTCTGCTGAGGCCCCCATGTTCATATAGGCATGAACC
ATGAGAAGTATGACAACAGCCTCAAGATCGTCAGCAATGCCTCCTGTACCACCAACTGCTTAGCACCCCTGGCCAAAGCC
ATCTATGACAACTTTGGTATCATGGAAGGATTCATGACCACAGTCCACGCTATCACTGCCACCCAGAAGACTGTGGATGG
CCCCTCCGGGAAACTGTGGCATGATGGCTGTGTGGCTCTCCAGAACATCATCCCTGCATCTACTGGCACTGCCAAGGCTG
TGGGCAAGGTCATCCCCGAGCTGAACAGGAAGCTCACTGGCATGGCCTTCCATGTCCCCATTGCTAATGTGTCAGTTGTG
GACCTGACCCACCGTCTGGAGAAACCTGCCAAATATGATGATATCAAGAAGGTGGTGAAGCAGGCGTCAGAGGGA

ORF - retro_pabe_1779 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.16 %
Parental protein coverage: 79.4 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKVKVGINGFGRIGR-LVTRAAFNSGKV-DIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVIN
KVK....GFG..GR.LVTRAAF.SGKV....AINDP..DLNY.VYMF.YDSTH.K.HGT.KAENGKLVIN
RetrocopyKVKAQVKGFGSTGR<LVTRAAFDSGKV<SVLAINDPSLDLNYIVYMFPYDSTHSKSHGTIKAENGKLVIN
ParentalGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAPSADAPMFV-MGVNHEK
GNPI.IF.E.DP.KIKWG.AGAEY..EST..FTTMEKAGAHLQ.GAKRVIISA.SA.APMF...G.NHEK
RetrocopyGNPISIF*E*DPTKIKWGHAGAEYIMESTSIFTTMEKAGAHLQQGAKRVIISALSAEAPMFI<IGMNHEK
ParentalYDNSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGALQNIIPA
YDNSLKIVSNASCTTNCLAPLAK.I.DNFGI.EG.MTTVHAITATQKTVDGPSGKLW.DG..ALQNIIPA
RetrocopyYDNSLKIVSNASCTTNCLAPLAKAIYDNFGIMEGFMTTVHAITATQKTVDGPSGKLWHDGCVALQNIIPA
ParentalSTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKAAKYDDIKKVVKQASEG
STG.AKAVGKVIPELN.KLTGMAF.VP.ANVSVVDLT.RLEK.AKYDDIKKVVKQASEG
RetrocopySTGTAKAVGKVIPELNRKLTGMAFHVPIANVSVVDLTHRLEKPAKYDDIKKVVKQASEG

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 .36 RPM 972 .32 RPM
SRP007412_heart 0 .15 RPM 1118 .01 RPM
SRP007412_kidney 0 .20 RPM 892 .74 RPM
SRP007412_liver 0 .15 RPM 668 .25 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1779 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1779 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1779 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2414
Pan troglodytes retro_ptro_1390
Macaca mulatta retro_mmul_605

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



Copyright © RetrogeneDB 2014-2017