RetrogeneDB ID: retro_meug_311

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold10067:30573..31152(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSMEUG00000004825
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_meug_311
GATATCCTTACATATGTCACCTGGAAACTGAGTGGCCTGCCAAAGCGCCGGGTGATTGGTAGTGGATGCAGTCTGGATTC
TACCAGATTCCACTATCTTATGTCTGAAAAACTTGGCATCCATCCAAGCAGCTGCCATGGCTGGATCCTTGGAGAGCACG
GGGACTCAAGTGTGGCTGTGTGGAGTGGAGTGAATGTGGCAGGCGTTTCCCTCCAAGACCTGAATCCAGAAATGGGAACT
GATAACAACAGTGAAAACTGGAAGGAGGTTCATAAGCTGGTGATTGAAAGTGTCTAGGAAGTGATCAAACTCAAAGGATA
CACTAACTGGGCTATTGGATTAAGTGCTGCTGATCTAATTGAGACCATGTTAAAAAATCTCTCCAAGATTCATCCCGTAT
CCACTATGGTGAAGGGGATGTATGGCATCGAGAATGAAGTTTTCCTTAGCCTTCCATGCATTCTGAATACCCAAGGACTG
ACCAGCGTTATCAACCAGAAGCTGAAAGATGATGAGGTAGCTCAACTCAAGAAGAGTGCAGATACCTTGTGGGACATCCA
GAAAGACCTGAAAGACCTG

Alignment

ORF - retro_meug_311 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.82 %
• Parental protein coverage: 57.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMSEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVS
          DILTYVTWKLSGLPK.RVIGSGC.LDS.RF.YLMSEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVS
Retrocopy DILTYVTWKLSGLPKRRVIGSGCSLDSTRFHYLMSEKLGIHPSSCHGWILGEHGDSSVAVWSGVNVAGVS

Parental  LQDLNPEMGTDNDSENWKEVHKLVIESAYEVIKLKGYTNWAIGLSVADLIETMLKNLSKIHPVSTMVKGM
          LQDLNPEMGTDN.SENWKEVHKLVIES..EVIKLKGYTNWAIGLS.ADLIETMLKNLSKIHPVSTMVKGM
Retrocopy LQDLNPEMGTDNNSENWKEVHKLVIESV*EVIKLKGYTNWAIGLSAADLIETMLKNLSKIHPVSTMVKGM

Parental  YGIENEVFLSLPCILNARGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL
          YGIENEVFLSLPCILN..GLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL
Retrocopy YGIENEVFLSLPCILNTQGLTSVINQKLKDDEVAQLKKSADTLWDIQKDLKDL

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_311 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_311 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 29 parental genes, and 169 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus	ENSBTAG00000019603	4 retrocopies	retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
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,
Choloepus hoffmanni	ENSCHOG00000007658	1 retrocopy	retro_chof_1145,
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,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Homo sapiens	ENSG00000111716	1 retrocopy	retro_hsap_4863,
Gorilla gorilla	ENSGGOG00000015758	1 retrocopy	retro_ggor_3033,
Loxodonta africana	ENSLAFG00000000972	2 retrocopies	retro_lafr_197, retro_lafr_315,
Macropus eugenii	ENSMEUG00000001462	91 retrocopies	retro_meug_101, retro_meug_1029, retro_meug_103, retro_meug_1082, retro_meug_1088, retro_meug_1105, retro_meug_1140, retro_meug_1162, retro_meug_1189, retro_meug_1190, retro_meug_1260, retro_meug_1288, retro_meug_1295, retro_meug_1301, retro_meug_1323, retro_meug_1329, retro_meug_1332, retro_meug_1356, retro_meug_1368, retro_meug_1376, retro_meug_1400, retro_meug_1402, retro_meug_1404, retro_meug_1417, retro_meug_1419, retro_meug_1420, retro_meug_1422, retro_meug_1484, retro_meug_1535, retro_meug_155, retro_meug_1556, retro_meug_1620, retro_meug_1632, retro_meug_1652, retro_meug_1674, retro_meug_1685, retro_meug_1720, retro_meug_1721, retro_meug_1747, retro_meug_1749, retro_meug_1765, retro_meug_1779, retro_meug_1781, retro_meug_181, retro_meug_1824, retro_meug_1875, retro_meug_1898, retro_meug_1906, retro_meug_1915, retro_meug_1927, retro_meug_1945, retro_meug_1977, retro_meug_200, retro_meug_2000, retro_meug_2022, retro_meug_2067, retro_meug_2107, retro_meug_2126, retro_meug_2137, retro_meug_2139, retro_meug_2168, retro_meug_226, retro_meug_244, retro_meug_291, retro_meug_336, retro_meug_351, retro_meug_436, retro_meug_448, retro_meug_477, retro_meug_532, retro_meug_572, retro_meug_590, retro_meug_591, retro_meug_626, retro_meug_634, retro_meug_638, retro_meug_639, retro_meug_660, retro_meug_68, retro_meug_736, retro_meug_737, retro_meug_832, retro_meug_861, retro_meug_867, retro_meug_870, retro_meug_891, retro_meug_916, retro_meug_927, retro_meug_971, retro_meug_980, retro_meug_981,
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,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805,
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,
Pongo abelii	ENSPPYG00000004356	3 retrocopies	retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
Pan troglodytes	ENSPTRG00000004762	1 retrocopy	retro_ptro_3237,
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,
Sorex araneus	ENSSARG00000002565	1 retrocopy	retro_sara_713,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501, retro_itri_648,
Tarsius syrichta	ENSTSYG00000013759	7 retrocopies	retro_tsyr_1130, retro_tsyr_1532, retro_tsyr_1860, retro_tsyr_2051, retro_tsyr_334, retro_tsyr_64, retro_tsyr_986,