RetrogeneDB ID: retro_chof_1869

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_40948:5781..6568(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHB
• Ensembl ID: ENSCHOG00000010050
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit [Source:HGNC Symbol;Acc:4803]

Sequence

>retro_chof_1869
CCCGCCATGGCAGAGTTCTCCACCAGCGAGACCATGGGCTGCTCCACAGACCAACTGGCTGCTGCCTTTGCTGTGTCATG
AGGGGAACAGGATGAGTACGTGCTGCGGTCCACAGTCTGTCCAAGAAGTCACAGGATGAAGGGCTCCTGTCAGACGTGGT
GCCCTTAAAAGTGCCAGGAAAAGATACAGTTACCAAAGATAATGGTATTCATCCTTCCTACCTGGAGCAGATGGCCAAGC
TGAGGCCCGCATTCATCAAGCCCTATGGCACGCTGACAGTTGCAAATTCTTCATTCCTAACCGACAGCGCCTGTGCAATG
CTCATGATGGCTGAGGAAAAGGCTGTGGCCATGGGGTACAAGCCCACAGCCTATCTGAGGGATTTTGTTTATGTATCTCA
GGATCCAAAAGATCAACTTTTACTTGGACCAAGATATGCTACTCCAAAAGTTCTAGAGAGAGCAGGATTAACAATGAATG
ATCTTGATGCTTTTGAATTTCATGAAGTTTTCTCTGGTCAGATTTTGGCTAATTTTAAAGCCATGGATTCTGATTGGTTT
CCACAAAACTACATGGGCAGAAAAACCAAGGTTGTACTGCCTCCCCTGGAGAAGTTTAATACCTGGGTGGATTGCTGTCC
CTGGGGCACCTGTTTGGAGCCACCGGCTGCCAGTTGGTCATAGCAGCTGCTAACAGGTTATGGAAGGAAGGAGGCCAGTA
CAGCCTAGTGGCTGCCTGTATGGCCGGAGGGCAGGGCCATGCTATGATAGAGGAAGCTTATCCAAAA

Alignment

ORF - retro_chof_1869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 64.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PAVAEFSTSETMGHSADRLAAAFAVPRREQDEYALRS-HSLAKKAQDEGLLSDVVPFKVPGKDTVTKDNG
          PA.AEFSTSETMG.S.D.LAAAFAV...EQDEY.LRS.HSL.KK.QDEGLLSDVVP.KVPGKDTVTKDNG
Retrocopy PAMAEFSTSETMGCSTDQLAAAFAVS*GEQDEYVLRS<HSLSKKSQDEGLLSDVVPLKVPGKDTVTKDNG

Parental  IRPSSLEQMAKLRPAFIKPYGTVTAANSSFLTDGASAVLMMAEEKALAMGYKPKAYLRDFVYVSQDPKDQ
          I.PS.LEQMAKLRPAFIKPYGT.T.ANSSFLTD.A.A.LMMAEEKA.AMGYKP.AYLRDFVYVSQDPKDQ
Retrocopy IHPSYLEQMAKLRPAFIKPYGTLTVANSSFLTDSACAMLMMAEEKAVAMGYKPTAYLRDFVYVSQDPKDQ

Parental  LLLGPTYATPKVLERAGLTMNDVDAFEFHEAFSXXXXXXXXXXXSDWFAQNYMGRKTKVGLPPMEKFNTW
          LLLGP.YATPKVLERAGLTMND.DAFEFHE.FS...........SDWF.QNYMGRKTKV.LPP.EKFNTW
Retrocopy LLLGPRYATPKVLERAGLTMNDLDAFEFHEVFSGQILANFKAMDSDWFPQNYMGRKTKVVLPPLEKFNTW

Parental  -GGSLSLGHPFGATGCRLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYPK
          .GG.LSLGH.FGATGC.LV.AAANRL.KEGGQY.LVAAC.AGGQGHAMI.EAYPK
Retrocopy <GGLLSLGHLFGATGCQLVIAAANRLWKEGGQYSLVAACMAGGQGHAMIEEAYPK

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_1869 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	ENSAMEG00000002288	1 retrocopy	retro_amel_1473,
Canis familiaris	ENSCAFG00000029395	1 retrocopy	retro_cfam_2114,
Choloepus hoffmanni	ENSCHOG00000010050	3 retrocopies	retro_chof_122, retro_chof_1869 , retro_chof_911,
Homo sapiens	ENSG00000138029	1 retrocopy	retro_hsap_4778,
Gorilla gorilla	ENSGGOG00000025829	1 retrocopy	retro_ggor_2976,
Microcebus murinus	ENSMICG00000006750	1 retrocopy	retro_mmur_1315,
Mus musculus	ENSMUSG00000059447	2 retrocopies	retro_mmus_1427, retro_mmus_1961,
Otolemur garnettii	ENSOGAG00000005444	1 retrocopy	retro_ogar_167,
Pongo abelii	ENSPPYG00000012582	1 retrocopy	retro_pabe_3718,
Pan troglodytes	ENSPTRG00000011733	1 retrocopy	retro_ptro_3180,
Tarsius syrichta	ENSTSYG00000003570	2 retrocopies	retro_tsyr_1316, retro_tsyr_1951,