RetrogeneDB ID: retro_chof_1225

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_2309:28944..29637(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSCHOG00000003153
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:4907]

Sequence

>retro_chof_1225
ATGGCAGCCTCCTTAAGGCTCCTAGGAGCCGCTTCCAGCTTCTGTACTCGAGCTGCAGGCAGTGGCCGGCTGTACCCGGC
CTTGCAGCGGTGTGTTCTAGGTCAACGGCTTCTAAGACTCCAATTGGATTCATCTGACTGGGCAACATGGGAAATCCCAT
GGCAAAATAAATCTCATGAAACATGGCTATCCGCTCATTCTTTATGATGTGTTCCCTGACACGTGCAAAGAGTTTCAAGA
ACGAGGTGAACATGTGGTGTCTTTCCCAGCAGAGGTAGCTGAAAAAGCTGACCGAATTATCACAGTGCTGCCCACAAGTA
TCAATGCAATTGAAGTTTATTCTGGAAAAAATGGAATTCTAAAGAAAGTGAAGAAAGGCTCATTATTAATAGATTCCAGT
ACACTCGATCCCAGCGTTTCAAAACAAATTGGCCAAAGAAGTTGAGAAAATGGGAGTACTTTTCATGGATGTCCCTATTT
CTGGCATGTGGAATCTGCTGGGTCTGGGGACCTCACAGTTTTGGGGGGAGGAGTGAAGAAGAATTTGCTGCTGCCCAAGA
GTTGCTGGGTTGCATGGGCTCAAGTGTGGTACATTGTGGAGGTATTGGAACTGGGCAGGCTGCAAAGATCTGCAACAACT
TGCTCTTAGTGATTAGTGTGATTGGAACTGCTGAAGCTGTAAATCTTGGAATC

Alignment

ORF - retro_chof_1225 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.95 %
• Parental protein coverage: 68.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAVFLRLRGAASSF-QYWSRRHWPAAPGLVAVCSRSMASKTPIGFIGLGNM-GNPMAK-NLMKHGYPLII
          MA..LRL.GAASSF..Y.S.R.WPA.PGL.AVCSRS.ASKTPIGFI.LGNM.G....K.NLMKHGYPLI.
Retrocopy MAASLRLLGAASSF<LYSSCRQWPAVPGLAAVCSRSTASKTPIGFI*LGNM<GKSHGKINLMKHGYPLIL

Parental  YDVFPDAC-EFQEQGEQVVSSPADVAEKADRIITMLPTSINAIEVYSGANGILKKVKKGSLLIDSSTIDP
          YDVFPD.C.EFQE.GE.VVS.PA.VAEKADRIIT.LPTSINAIEVYSG.NGILKKVKKGSLLIDSST.DP
Retrocopy YDVFPDTCKEFQERGEHVVSFPAEVAEKADRIITVLPTSINAIEVYSGKNGILKKVKKGSLLIDSSTLDP

Parental  TVSKE-LAKEVEKMGAVFMDAPVSG-GVGAARSGNLTFMVGGV-EEEFAAAQQLLGCMGSNVVYCGAVAT
          .VSK..LAKEVEKMG..FMD.P.SG..V..A.SG.LT...GGV.EEEFAAAQ.LLGCMGS.VV.CG...T
Retrocopy SVSKQ>LAKEVEKMGVLFMDVPISG<HVESAGSGDLTVLGGGV<EEEFAAAQELLGCMGSSVVHCGGIGT

Parental  ARAAKICNNMLLAISMIGTAEAMNLGI
          ..AAKICNN.LL.IS.IGTAEA.NLGI
Retrocopy GQAAKICNNLLLVISVIGTAEAVNLGI

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_1225 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005849	1 retrocopy	retro_amel_678,
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225 ,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Microcebus murinus	ENSMICG00000000512	1 retrocopy	retro_mmur_1059,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136,
Tursiops truncatus	ENSTTRG00000015276	4 retrocopies	retro_ttru_124, retro_ttru_150, retro_ttru_589, retro_ttru_807,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571,