RetrogeneDB ID:

retro_lafr_954

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_51:359717..360517(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000031522
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GAPDH
Ensembl ID:ENSLAFG00000002780
Aliases:None
Description:Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G3SR49]


Retrocopy-Parental alignment summary:






>retro_lafr_954
ATCAATGGAAAGCCCATCCCTATCTTCCAGGAGTACAATCCCTCCAATGTCATGTGGGGTGATGCTGGTGCCGAATATGT
TGTAGAGTTCAACGGTGTCTTCACAGCCTCATGAGAAGGCTGAGCCTCACTCGAAGAGTGGTGCCAAAGGGATAATCATC
TCTGCCCCTTCTGCCAATGCCTCATGTGTGTGATGGGTGTGAACCATGAGAAGCATGACAACTTCCTCAAGGTTGTCAAC
AATACCTCCTTTGCCACCAACTGCTTAGCTCCCCCAGCCAAGGTCATCCATGACAACTTTGGCACCATAGAGGGTCTCAT
GACCACAGTCCATGACATCCCGCCACCCAGAAGATTGCAGATGGCCCCTTTGTGAAATTGTGGCATGAATGCCAGGAGGC
TGCTCAGAACATCACCCCTGTATCTACTGGTGCTGACAAGGCTGTGGGCAAGGTCATCACTGAGCTGAATGGGAAGTTCA
CTGGCATGGCCTTTGTGTCCTCACCCCGCAATGTGTCAGTTGTGGATCTGACCTGTCCTCTGGAGAAAATTGCCAAATAC
AATTACATCAAGAAGGTGGTGAAGCAGGCACAAGAGGGTCCCCTAAAGGGCATCCTCAGCTGTACTGACGACAAGGTTGT
CTCCTGAGACTTTAACAGTGGCACTCACTCTTACACCTTTGATGCTGAAGCTGGCATTGCCCTCAACTACCACTTTGTCA
AGCTCATTTCCTGATATGAAAATGAATTTTGCTACAACAACAGGGTGGTGGAATTTATGGTCCACATGGTCTCCAAGGAA

ORF - retro_lafr_954 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.85 %
Parental protein coverage: 82.15 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalINGKPISIFQERDPANIKWGDAGAEYVVESTGVFTTL-EKAGAHLKGGAKRVIISAPSADAP-MFVMGVN
INGKPI.IFQE..P.N..WGDAGAEYVVE..GVFT...EKA..H.K.GAK..IISAPSA.A..M.VMGVN
RetrocopyINGKPIPIFQEYNPSNVMWGDAGAEYVVEFNGVFTAS>EKAEPHSKSGAKGIIISAPSANAS<MCVMGVN
ParentalHEKYDNSLKIVSNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAIT-ATQKTVDGPSGKQWRDGRGAAQN
HEK.DN.LK.V.N.S..TNCLAP.AKVIHDNFG..EGLMTTVH.I..ATQK..DGP..K.W.....AAQN
RetrocopyHEKHDNFLKVVNNTSFATNCLAPPAKVIHDNFGTIEGLMTTVHDIP<ATQKIADGPFVKLWHECQEAAQN
ParentalIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTPNVSVVDLTCRLEKAAKYDDIKKVVKQASEGPLKGILG
I.P.STGA.KAVGKVI.ELNGK.TGMAF.....NVSVVDLTC.LEK.AKY..IKKVVKQA.EGPLKGIL.
RetrocopyITPVSTGADKAVGKVITELNGKFTGMAFVSSPRNVSVVDLTCPLEKIAKYNYIKKVVKQAQEGPLKGILS
ParentalYTEDQVVSCDFNSDSHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMVHMASKE
.T.D.VVS.DFNS..HS.TFDA.AGIALN.HFVKLIS.Y.NEF.Y.NRVV..MVHM.SKE
RetrocopyCTDDKVVS*DFNSGTHSYTFDAEAGIALNYHFVKLIS*YENEFCYNNRVVEFMVHMVSKE

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






Loxodonta africana was not studied using RNA-Seq expression data.
Loxodonta africana was not studied using ChIP-Seq data.
Loxodonta africana was not studied using EST data.
Loxodonta africana was not studied using FANTOM5 data.
retro_lafr_954 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana 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 34 parental genes, and 769 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000066755 retrocopies
Ailuropoda melanoleuca ENSAMEG0000001432935 retrocopies
Bos taurus ENSBTAG000000147314 retrocopies
Canis familiaris ENSCAFG000000150774 retrocopies
Callithrix jacchus ENSCJAG000000082341 retrocopy
Cavia porcellus ENSCPOG000000263501 retrocopy
Equus caballus ENSECAG0000002205111 retrocopies
Erinaceus europaeus ENSEEUG000000114443 retrocopies
Echinops telfairi ENSETEG00000013749118 retrocopies
retro_etel_1011, retro_etel_1037, retro_etel_1070, retro_etel_1117, retro_etel_1132, retro_etel_1153, retro_etel_1171, retro_etel_1183, retro_etel_1214, retro_etel_1215, retro_etel_1247, retro_etel_1249, retro_etel_1255, retro_etel_1257, retro_etel_1258, retro_etel_1266, retro_etel_127, retro_etel_1320, retro_etel_1349, retro_etel_1352, retro_etel_1381, retro_etel_1386, retro_etel_1389, retro_etel_1408, retro_etel_1419, retro_etel_1422, retro_etel_1431, retro_etel_1437, retro_etel_1470, retro_etel_1473, retro_etel_1490, retro_etel_150, retro_etel_1511, retro_etel_1538, retro_etel_1550, retro_etel_1563, retro_etel_1570, retro_etel_1588, retro_etel_1601, retro_etel_1608, retro_etel_1620, retro_etel_163, retro_etel_1635, retro_etel_1641, retro_etel_1674, retro_etel_1679, retro_etel_1702, retro_etel_1738, retro_etel_1746, retro_etel_1759, retro_etel_1769, retro_etel_1776, retro_etel_1780, retro_etel_180, retro_etel_184, retro_etel_1840, retro_etel_1869, retro_etel_1895, retro_etel_1897, retro_etel_1949, retro_etel_1970, retro_etel_1976, retro_etel_1982, retro_etel_1989, retro_etel_2033, retro_etel_2076, retro_etel_209, retro_etel_212, retro_etel_213, retro_etel_2152, retro_etel_2161, retro_etel_2173, retro_etel_2198, retro_etel_2202, retro_etel_2210, retro_etel_243, retro_etel_290, retro_etel_330, retro_etel_339, retro_etel_340, retro_etel_365, retro_etel_397, retro_etel_432, retro_etel_440, retro_etel_463, retro_etel_489, retro_etel_495, retro_etel_504, retro_etel_536, retro_etel_557, retro_etel_586, retro_etel_589, retro_etel_600, retro_etel_611, retro_etel_618, retro_etel_621, retro_etel_624, retro_etel_649, retro_etel_653, retro_etel_69, retro_etel_770, retro_etel_780, retro_etel_790, retro_etel_792, retro_etel_798, retro_etel_802, retro_etel_810, retro_etel_874, retro_etel_895, retro_etel_899, retro_etel_90, retro_etel_906, retro_etel_931, retro_etel_934, retro_etel_935, retro_etel_968, retro_etel_969, retro_etel_987,
Felis catus ENSFCAG0000000687417 retrocopies
Homo sapiens ENSG0000011164042 retrocopies
Gorilla gorilla ENSGGOG0000000955330 retrocopies
Loxodonta africana ENSLAFG00000002780 3 retrocopies
retro_lafr_421, retro_lafr_46, retro_lafr_954 ,
Macropus eugenii ENSMEUG0000001527367 retrocopies
Microcebus murinus ENSMICG0000000654616 retrocopies
Myotis lucifugus ENSMLUG0000001432018 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,
Nomascus leucogenys ENSNLEG0000000382544 retrocopies
Ornithorhynchus anatinus ENSOANG000000044921 retrocopy
Ochotona princeps ENSOPRG0000001251410 retrocopies
Procavia capensis ENSPCAG000000069289 retrocopies
Pongo abelii ENSPPYG0000000418938 retrocopies
Pan troglodytes ENSPTRG0000000457743 retrocopies
Pteropus vampyrus ENSPVAG0000001257014 retrocopies
Rattus norvegicus ENSRNOG000000186304 retrocopies
Rattus norvegicus ENSRNOG000000306382 retrocopies
Sarcophilus harrisii ENSSHAG000000149534 retrocopies
Sus scrofa ENSSSCG000000006942 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000075389 retrocopies
Tursiops truncatus ENSTTRG000000160942 retrocopies
Xenopus tropicalis ENSXETG000000339751 retrocopy



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