RetrogeneDB ID: retro_etel_850

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_175715:6250..6841(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSETEG00000019955
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_etel_850
ATGGCAACCCTTAAGGACAAGCCAATTGTACCCGCTGCAGAAGAGGCACTGGTTCCAAACAATAAGATCACTGTGGTCCG
GGTTGGACAAGCGGGTATGGCATGTGCCATCAGCATTCTGGGAAAGTCCCTGGCTGATGAACTGGCCCTTGTGGATGTTT
TGGAAGATAAACTCAAAGGAGAAATGATGGATCTGCAGCATGGGAGCTTATTTCTCCAGGCACCTAAAACCGTAGCGGAT
AAAGATTCCTCTGTGACGGCCAGTTCTAAGACTGTGGTGGTGACTGCAGGAGTCCGTCAGCAAGAGGCGGAGAGTCGGCT
CAATCTGGTGCAGAGGAATGTCAATGTCTTCAAGTTCATTATTCCTCAGATCGTCAAGTACAGCCCCGACTGCATCATAA
TTGTGGTGTCCAATCCAGTGGCTATTCTTACATACGTTACCTGGAAACTAAGTGGATTGCCCAAGCACTGTATGATTGGA
AGTGACTGTAACCTGGATTCTGCTAGATTTCGCTATCTGATGGCTGAAAAACTTGGCATTCATCCCAGCAGCTGCCATGG
ATGGATGTTGGGAGCGCATGGAGACTCGAGT

Alignment

ORF - retro_etel_850 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.4 %
• Parental protein coverage: 59.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLKNKLIAPVAEEEALVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS
          MATLK.K.I.P.AEE.ALVPNNKITVV.VGQ.GMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS
Retrocopy MATLKDKPIVPAAEE-ALVPNNKITVVRVGQAGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS

Parental  LFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
          LFLQ.PK.VADKD.SVTA.SK.VVVTAGVRQQE.ESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
Retrocopy LFLQAPKTVADKDSSVTASSKTVVVTAGVRQQEAESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP

Parental  VDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSS
          V.ILTYVTWKLSGLPKH..IGS.CNLDSARFRYLMAEKLGIHPSSCHGW.LG.HGDSS
Retrocopy VAILTYVTWKLSGLPKHCMIGSDCNLDSARFRYLMAEKLGIHPSSCHGWMLGAHGDSS

Legend:

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

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_850 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 21 parental genes, and 65 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,
Echinops telfairi	ENSETEG00000007508	15 retrocopies	retro_etel_1091, retro_etel_1192, retro_etel_1243, retro_etel_1309, retro_etel_1439, retro_etel_1609, retro_etel_1870, retro_etel_1916, retro_etel_1969, retro_etel_1996, retro_etel_2209, retro_etel_361, retro_etel_392, retro_etel_828, retro_etel_884,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850 ,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Homo sapiens	ENSG00000111716	1 retrocopy	retro_hsap_4863,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
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,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805,
Pongo abelii	ENSPPYG00000004356	3 retrocopies	retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
Pan troglodytes	ENSPTRG00000004762	1 retrocopy	retro_ptro_3237,
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,