RetrogeneDB ID:

retro_nleu_999

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397278.1:26806797..26807591(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSNLEG00000003825
Aliases:None
Description:Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G1QVR0]


Retrocopy-Parental alignment summary:






>retro_nleu_999
AACGGAAATCCCATCACCATCTTCCAGGAGTGAGATCCCACCAAAATCAAACAGGATGATGTTGGTGCTGATTATGTTAT
GGAGTCCACTGGCATCTTCACTACCATGGAGAAGGCTGGGGCTCACTTAGAGGGGAGAGCCAAAAGGGTCATTACCTCTG
CCCCCTCTGCTGATACCCCCATGTTCGTGATGGGCATGAGCCATAAGAAGTATAAAAACTTCAAGATCATCAGCAATGCC
TCCTGCACCACCGGCTGCCTAACCCCCTGGCCAAGGTCATCCATAATAACTCTGGCATCATGAAGCGACTCAGGATCACA
GTCCATGCCATCACTGCTAACCAGAGGACTGTCATGGCCCCTCTGGGAAACTGTGTTGTGATGGCTATGGGGCTCTCCAT
TACGTCATCCCTGCATGTGTCTATTGGTGCTGCCAAGGCTGTGGGCAAGGTCATCCCCAAGCCGAACAGGAAGCTCAATG
GTATGGCCTTCCATGTACCCACTGCCAATGTGTCAGTCATGGACCTGACCTGCTCTCTGGAGAAACCAGCCAAATATGAT
GACATCAAGGAGGTGGTGAAGCGGCATCAGAAGGGGCCCTCAGGGGCATCGTGGGCCACAACTGAGCACCAGGCTGTCTC
CTCCAACTATAACAGTGACACCCACTCTTCCACCTTCAACATTGGGGCTGGCATTGCCCTCAACCTCTTTGTCAGGCTCA
TTTCCGGGTATGACAATGAATTTGGCTACAGCAACAAAGTGATAACCTTCATGATCCACATGGCTTCCAAGAAG

ORF - retro_nleu_999 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70. %
Parental protein coverage: 79.4 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalNGNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAPSADAPMFVMGVNHEK
NGNPITIFQE.DP.KIK..D.GA.YV.ESTG.FTTMEKAGAHL.G.AKRVI.SAPSAD.PMFVMG..H.K
RetrocopyNGNPITIFQE*DPTKIKQDDVGADYVMESTGIFTTMEKAGAHLEGRAKRVITSAPSADTPMFVMGMSHKK
ParentalYDNSLKIVSNASCTTNCLAP-LAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRG-ALQNII
Y.N..KI.SNASCTT.CL.P.LAKVIH.N.GI...L..TVHAITA.Q.TV..P.G.......G.......
RetrocopyYKN-FKIISNASCTTGCLTP<LAKVIHNNSGIMKRLRITVHAITANQRTVMAPLGNCVVMAMGLSITSSL
ParentalPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQ-ASEGPLKGILGY
..S.GAAKAVGKVIP..N.KL.GMAF.VPTANVSV.DLTC.LEKPAKYDDIK.VVK..ASEG.L.GI.G.
RetrocopyHVSIGAAKAVGKVIPKPNRKLNGMAFHVPTANVSVMDLTCSLEKPAKYDDIKEVVKR<ASEGALRGIVGH
Parental-TEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMSHMASKE
.TEHQ.VSS..NSDTHSSTF..GAGIALN..FV.LIS.YDNEFGYSN.V...M.HMASK.
Retrocopy>TEHQAVSSNYNSDTHSSTFNIGAGIALN-LFVRLISGYDNEFGYSNKVITFMIHMASKK

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






Nomascus leucogenys was not studied using RNA-Seq expression data.
Nomascus leucogenys was not studied using ChIP-Seq data.
Nomascus leucogenys was not studied using EST data.
Nomascus leucogenys was not studied using FANTOM5 data.
retro_nleu_999 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 16 parental genes, and 367 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
Loxodonta africana ENSLAFG000000027803 retrocopies
Macropus eugenii ENSMEUG0000001527367 retrocopies
Microcebus murinus ENSMICG0000000654616 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,
Nomascus leucogenys ENSNLEG00000003825 44 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



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