RetrogeneDB ID: retro_lafr_315

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_12:54545218..54545982(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSLAFG00000000972
• Aliases: None
• Description: None

Sequence

>retro_lafr_315
AGCTTATTTCTTCAGACACCTCAAATCGTAACAGATAAAGATTACTCTGTGATGGCCAATTCTCAGACTGTGGTGGTAAC
AGCAGGAGTTCATCAGCAAGCGGGGGAGAGTCATCTCAATCTGGTGCAGAGGAATGTTAATGTCTTCAAACTCACTATTC
CTCAGATCATCAAGTACAGTCCCAACTGCATCGTAATTGTGGTTTCCAACCCAGCAAGTATTCTTACATATGTTACCTGG
AAACTAAGTGGATTACCCAAGCACCGTGCGATTGGAAGTGGTTGTAACCTGGATTCTGCTAGATTTTGCTATCATATGGC
TGAAAAACTTGGCATTCATCCCAGGAGCTGCCATGGATGGATTTTGGGAAAACATAACAACTCAAGTGTGGCAGTGTAGA
GTGGCGTGAACATGGCAGGGGTTTCTTTCCAGGAACTAAATCCAGAGAGGAGGACAGACAATGACAGTGAAGACTGGGAG
GAAGTGCATAAAATGGTGGTTGAAAGTGCCTATGAAATCATCAAGCTAAAAGGATACACCACCTGGGCTACTGGATTAAG
TGTGGCTGATCTGATTGAATCCATGTTGAAAACCTATCCAGGATTCACCCAGTGTCAACGATGATGAAGAGGATGGATAG
CATTGAGAATGAAGTCTTCCTGAGCCTACCATGTATCCTGAATGGTTGGGGGTTAACAAGTGTTATCAACCAGAAGCTGA
AGGATGATGAGGTTGTTGAACCCGAGAAGAGCACAGACACTGTG

Alignment

ORF - retro_lafr_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.64 %
• Parental protein coverage: 76.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLFLQTPKIVADKDYSVTANSKVVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSN
          SLFLQTP.IV.DKDYSV.ANS..VVVTAGV.QQ.GES.LNLVQRNVNVFK..IPQI.KYSP.CI.IVVSN
Retrocopy SLFLQTPQIVTDKDYSVMANSQTVVVTAGVHQQAGESHLNLVQRNVNVFKLTIPQIIKYSPNCIVIVVSN

Parental  PVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAG
          P..ILTYVTWKLSGLPKHR.IGSGCNLDSARF.Y.MAEKLGIHP.SCHGWILG.H..SSVAV.SGVN.AG
Retrocopy PASILTYVTWKLSGLPKHRAIGSGCNLDSARFCYHMAEKLGIHPRSCHGWILGKHNNSSVAV*SGVNMAG

Parental  VSLQELNPEMGTDNDSENWKEVHKLVVESAYEVIKLKGYTNWAIGLSVADLIESMLK-NLSRIHPVSTMV
          VS.QELNPE..TDNDSE.W.EVHK.VVESAYE.IKLKGYT.WA.GLSVADLIESMLK.NLSRIHPVSTM.
Retrocopy VSFQELNPERRTDNDSEDWEEVHKMVVESAYEIIKLKGYTTWATGLSVADLIESMLK<NLSRIHPVSTMM

Parental  KGMYGIENEVFLSLPCVLNARGLTSVINQKLKDDEVAQLKKSADTL
          K.M..IENEVFLSLPC.LN..GLTSVINQKLKDDEV....KS.DT.
Retrocopy KRMDSIENEVFLSLPCILNGWGLTSVINQKLKDDEVVEPEKSTDTV

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_315 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 57 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Dasypus novemcinctus	ENSDNOG00000013620	4 retrocopies	retro_dnov_1161, retro_dnov_1511, retro_dnov_1570, retro_dnov_529,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Gorilla gorilla	ENSGGOG00000015758	1 retrocopy	retro_ggor_3033,
Loxodonta africana	ENSLAFG00000000972	2 retrocopies	retro_lafr_197, retro_lafr_315 ,
Loxodonta africana	ENSLAFG00000011307	1 retrocopy	retro_lafr_11,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Microcebus murinus	ENSMICG00000017183	2 retrocopies	retro_mmur_275, retro_mmur_300,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mus musculus	ENSMUSG00000030246	4 retrocopies	retro_mmus_1817, retro_mmus_2035, retro_mmus_2509, retro_mmus_335,
Otolemur garnettii	ENSOGAG00000004763	9 retrocopies	retro_ogar_1469, retro_ogar_2093, retro_ogar_2344, retro_ogar_2459, retro_ogar_3288, retro_ogar_3342, retro_ogar_3383, retro_ogar_689, retro_ogar_721,
Pteropus vampyrus	ENSPVAG00000002462	3 retrocopies	retro_pvam_1487, retro_pvam_320, retro_pvam_673,
Rattus norvegicus	ENSRNOG00000013000	3 retrocopies	retro_rnor_2697, retro_rnor_2749, retro_rnor_2834,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,