RetrogeneDB ID: retro_chof_1145

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_210971:1359..1953(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSCHOG00000007658
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_chof_1145
ATGGCCATTCTTAAGGAAAAACTGATTTGCACCAGTTGCAGAAGAAGAGGCAACAGTCCCAAACAATAAGATCACTGTAG
TGGGCATCAGAGAAGTTGGTATGGTATGTGCCATCAGCATTCTCGGAAAGTCTCTAACAGATGAACTTGCCCTTGTGGTT
GTTTTGGAAGATAAACTCAAAGGAAAAATGATGATCTGCAGCATGGAAGCTTATTTCTTCAAACACCTAAAATTGTGGCA
GATAAAGATTACTCTGTGACTGCTAATTCTAAGATTGTGGTGGTAACTGCAGGAGTCCATCAGCAAGAGGGCAAGAGTTG
CCTCGATCTCATTCAGAGGAACGTTAATGTCTTCAAATTCATTATTCCTCAGATAGTCAAGTACAGTCCTGACTGCATCA
TAATTGTGGTTTCCAACCCAGTGGATATTCTAATCTACGTTACCTGGAAACTAAGTGGCTTACCCAAGCACCGTGTGATT
GGAAGTGGGTACAATCTGGATTCTGCTAGATTTTGTTATCTTATGGCTGAAAAACTTGGCATTCATCCCAGCAGCTGTCA
TAGATGGATTTTGGGAGAAAACGGCGACTCAAGC

Alignment

ORF - retro_chof_1145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 59.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATLKEKLI-APVGEEEATVPNNKITVVGVGQVGMACAISILGKSLTDELALVDVLEDKLKGEMM-DLQH
          MA.LKEKLI.APV.EEEATVPNNKITVVG...VGM.CAISILGKSLTDELALV.VLEDKLKG.MM.DLQH
Retrocopy MAILKEKLI>APVAEEEATVPNNKITVVGIREVGMVCAISILGKSLTDELALVVVLEDKLKGKMM<DLQH

Parental  GSLFLQTPKIVADKDYSVTANSKIVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVS
          GSLFLQTPKIVADKDYSVTANSKIVVVTAGV.QQEG.S.L.L.QRNVNVFKFIIPQIVKYSPDCIIIVVS
Retrocopy GSLFLQTPKIVADKDYSVTANSKIVVVTAGVHQQEGKSCLDLIQRNVNVFKFIIPQIVKYSPDCIIIVVS

Parental  NPVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSS
          NPVDIL.YVTWKLSGLPKHRVIGSG.NLDSARF.YLMAEKLGIHPSSCH.WILGE.GDSS
Retrocopy NPVDILIYVTWKLSGLPKHRVIGSGYNLDSARFCYLMAEKLGIHPSSCHRWILGENGDSS

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1145 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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 12 parental genes, and 43 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,
Choloepus hoffmanni	ENSCHOG00000007658	1 retrocopy	retro_chof_1145 ,
Choloepus hoffmanni	ENSCHOG00000009977	14 retrocopies	retro_chof_1038, retro_chof_144, retro_chof_1489, retro_chof_1524, retro_chof_1547, retro_chof_172, retro_chof_1874, retro_chof_2121, retro_chof_217, retro_chof_2365, retro_chof_2588, retro_chof_2611, retro_chof_552, retro_chof_990,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
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,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,