RetrogeneDB ID:

retro_lafr_491

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_19:32363002..32363648(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLAFG00000004598
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_491
ATGCCCATTGAAGCCACAGAAACCGTTCCTGCTACAGAGCAGGAGTTGCCACAACCTCAGGCTGAGACAGGGTCTGAAAC
AGAATTTGATGGTGATGAATTTGTACCAGAGCTCAAGGAACAGGAGTCCACACAGGCAACCACACAACAAGCCCAACCAG
CGGCAACAGCTGAAATCGATGAAGAACCAGTCAGTAAGGCAAAACAGAGTCCGAGCGAAAAGAAGACATGGAAGACTATG
TCCAAACTGGGTCTTCGACAAGTCACGGGGGTGACTAGAGTCACTATCCAGAAATCTAGGAATATCCTCTTTGTCATCAC
AAAGCCAGATGTCTACAAGAGCCCAGCTTCAGATACCTACCTAGTTTTGGGGGGAAGCCAAGATGGAAGATTTATCTCAG
CAAGCACAGCTGGCAGCTGCAGAGAAATTCAAAGTTCAAGGTGAAGCTGTCTCAAACATTCAAGAAAGCACACAAGCTCC
AACTGTACAAGAGGAGAGTGAAGAGGAAGAGGTTGACAAAACAGGTGTGGAAGTTTAGGACATAGAATTGGTCATGTCAC
AAGCAAGTATGTCAAGAGCAAAGATGGTCCGAGACCTGAAGACCAACAGTAATGATACTGTAAACGCTACTATGGAATTA
ACAATG

ORF - retro_lafr_491 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPGEATETVPATEQELPQPQAETGSGTESDSDESVPELEEQDSTQATTQQAQLAAAAEIDEEPVSKAKQS
MP.EATETVPATEQELPQPQAETGS.TE.D.DE.VPEL.EQ.STQATTQQAQ.AA.AEIDEEPVSKAKQS
RetrocopyMPIEATETVPATEQELPQPQAETGSETEFDGDEFVPELKEQESTQATTQQAQPAATAEIDEEPVSKAKQS
ParentalRSEKKARKAMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIV-FGEAKIEDLSQQAQLAA
.SEKK..K.MSKLGLRQVTGVTRVTI.KS.NILFVITKPDVYKSPASDTY.V..GEAK.EDLSQQAQLAA
RetrocopyPSEKKTWKTMSKLGLRQVTGVTRVTIQKSRNILFVITKPDVYKSPASDTYLV>WGEAKMEDLSQQAQLAA
ParentalAEKFKVQGEAVSNIQENTQTPTVQEESEEEEVDETGVEVKDIELVMSQANVSRAKAVRALKNNSNDIVNA
AEKFKVQGEAVSNIQE.TQ.PTVQEESEEEEVD.TGVEV.DIELVMSQA..SRAK.VR.LK.NSND.VNA
RetrocopyAEKFKVQGEAVSNIQESTQAPTVQEESEEEEVDKTGVEV*DIELVMSQASMSRAKMVRDLKTNSNDTVNA
ParentalIMELTM
.MELTM
RetrocopyTMELTM

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






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_491 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 24 parental genes, and 108 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041753 retrocopies
retro_amel_1725, retro_amel_1821, retro_amel_643,
Bos taurus ENSBTAG000000107012 retrocopies
retro_btau_1237, retro_btau_1620,
Canis familiaris ENSCAFG000000001418 retrocopies
retro_cfam_1502, retro_cfam_1561, retro_cfam_1884, retro_cfam_1913, retro_cfam_2096, retro_cfam_2169, retro_cfam_710, retro_cfam_974,
Callithrix jacchus ENSCJAG000000107018 retrocopies
retro_cjac_1063, retro_cjac_1452, retro_cjac_1875, retro_cjac_2202, retro_cjac_2453, retro_cjac_2696, retro_cjac_2975, retro_cjac_3232,
Cavia porcellus ENSCPOG000000126543 retrocopies
retro_cpor_1025, retro_cpor_1365, retro_cpor_617,
Dipodomys ordii ENSDORG000000145222 retrocopies
retro_dord_228, retro_dord_699,
Equus caballus ENSECAG000000152421 retrocopy
retro_ecab_785,
Erinaceus europaeus ENSEEUG000000104585 retrocopies
retro_eeur_170, retro_eeur_207, retro_eeur_242, retro_eeur_334, retro_eeur_520,
Homo sapiens ENSG000001965316 retrocopies
retro_hsap_3006, retro_hsap_3027, retro_hsap_3968, retro_hsap_3992, retro_hsap_737, retro_hsap_77,
Loxodonta africana ENSLAFG00000004598 6 retrocopies
retro_lafr_1107, retro_lafr_113, retro_lafr_1251, retro_lafr_166, retro_lafr_491 , retro_lafr_958,
Macropus eugenii ENSMEUG000000084123 retrocopies
retro_meug_1630, retro_meug_2063, retro_meug_2147,
Microcebus murinus ENSMICG000000164655 retrocopies
retro_mmur_1122, retro_mmur_450, retro_mmur_585, retro_mmur_684, retro_mmur_807,
Myotis lucifugus ENSMLUG0000000116916 retrocopies
retro_mluc_1147, retro_mluc_1653, retro_mluc_1668, retro_mluc_1756, retro_mluc_1767, retro_mluc_1851, retro_mluc_1881, retro_mluc_1941, retro_mluc_2587, retro_mluc_2600, retro_mluc_414, retro_mluc_492, retro_mluc_526, retro_mluc_641, retro_mluc_725, retro_mluc_861,
Macaca mulatta ENSMMUG000000030734 retrocopies
retro_mmul_1233, retro_mmul_1933, retro_mmul_2066, retro_mmul_889,
Mus musculus ENSMUSG000000613151 retrocopy
retro_mmus_968,
Nomascus leucogenys ENSNLEG000000174497 retrocopies
retro_nleu_1358, retro_nleu_20, retro_nleu_2522, retro_nleu_478, retro_nleu_754, retro_nleu_839, retro_nleu_941,
Ochotona princeps ENSOPRG000000017813 retrocopies
retro_opri_264, retro_opri_758, retro_opri_961,
Procavia capensis ENSPCAG000000070675 retrocopies
retro_pcap_150, retro_pcap_224, retro_pcap_282, retro_pcap_305, retro_pcap_324,
Pongo abelii ENSPPYG000000046706 retrocopies
retro_pabe_2507, retro_pabe_26, retro_pabe_3279, retro_pabe_633, retro_pabe_656, retro_pabe_764,
Pteropus vampyrus ENSPVAG000000080158 retrocopies
retro_pvam_1007, retro_pvam_1097, retro_pvam_1154, retro_pvam_1173, retro_pvam_1382, retro_pvam_1384, retro_pvam_290, retro_pvam_580,
Sarcophilus harrisii ENSSHAG000000021751 retrocopy
retro_shar_213,
Ictidomys tridecemlineatus ENSSTOG000000090281 retrocopy
retro_itri_367,
Tursiops truncatus ENSTTRG000000021502 retrocopies
retro_ttru_1157, retro_ttru_760,
Vicugna pacos ENSVPAG000000040282 retrocopies
retro_vpac_485, retro_vpac_611,


Copyright © RetrogeneDB 2014-2017