RetrogeneDB ID: retro_chof_1481

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_304071:554..1288(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTL6A
• Ensembl ID: ENSCHOG00000009477
• Aliases: None
• Description: actin-like 6A [Source:HGNC Symbol;Acc:24124]

Sequence

>retro_chof_1481
TGCGCTCATTGTCATTCTACTGGGTTGATTTTGGACAGTGGAGTCACTCATACCACTGCAATTCCAGTCCACGATGGCTA
TGTCCTTCAACAAGGCATTGTGAAATACCCTCTTACTGGAGACTTTATTATGAAGTGTGGAGAACTCTTCCAAGAAATGA
ATATAGAATTGATCCCTCCATATATGACTGCATCAAAAGAAGCTGTTCATGAAGGAACTCCAGTAAACTGGAAAAGAAAA
GAGAAGTTGCCACAGGTTACAAGGTCATGGCACAATTATATGTGTAATTGTGTTATCCAGGATTTTCAAGCTTTAGAACT
GCAAGTATCAGATTTCAACTTATGATGAACTAGTAGCTGCACAGATGCTAACTGTTCACTATGAATTTTCCAGTAGCTAT
AACTGTGATTTTGGTGCAGAACAGCTAAGGATTCCTGAAGGATTATTTGACCCTTCCAATATAAAAGGGTTTATCAGGAA
ATACAATGCTAGGAGTCAGTCACGTTGTCACCACAAGTGTTGGTTTTGTGATATTGGTATCAGACCAGGTCTCTATGGCA
GTGTGATAGTGGCAGGAGGAAACACGCTAATACAGAGCTTTACTGACAGGTTGAACAGAGAGCTCTCTCAAAAAACTACC
TCCCCCACCCCGTATGCGGTTGAAACATACAAGTAATACAACAGTTGAACGAAGGTTTAGTTCATGGATTGGTGGCTCCA
TTTTAGCTTCTTTG

Alignment

ORF - retro_chof_1481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.91 %
• Parental protein coverage: 60.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CKTAVLTAFACRTGLIWXXEANVVEFYVLQQGIVKSPLAGDFITMQCRELFQEMNIELIPPYMIASKEAV
          C.....T......G........V...YVLQQGIVK.PL.GDFI.M.C.ELFQEMNIELIPPYM.ASKEAV
Retrocopy CAHCHSTGLILDSGVTHTTAIPVHDGYVLQQGIVKYPLTGDFI-MKCGELFQEMNIELIPPYMTASKEAV

Parental  REGSPANWKRKEKLPQVTRSWHNYMCNCVIQDFQASVLQVSD-STYDEQVAAQMPTVHYEFPNGYNCDFG
          .EG.P.NWKRKEKLPQVTRSWHNYMCNCVIQDFQA..LQVSD.STYDE.VAAQM.TVHYEF...YNCDFG
Retrocopy HEGTPVNWKRKEKLPQVTRSWHNYMCNCVIQDFQALELQVSD>STYDELVAAQMLTVHYEFSSSYNCDFG

Parental  AERLKIPEGLFDPSNV-KGLSGNTMLGVSHVVTTSVG-MCDIDIRPGLYGSVIVAGGNTLIQSFTDRLNR
          AE.L.IPEGLFDPSN..KGLSGNTMLGVSHVVTTSVG..CDI.IRPGLYGSVIVAGGNTLIQSFTDRLNR
Retrocopy AEQLRIPEGLFDPSNI>KGLSGNTMLGVSHVVTTSVG<FCDIGIRPGLYGSVIVAGGNTLIQSFTDRLNR

Parental  ELSQKT-PPSMRLKL-IANNTTVERRFSSWIGGSILASL
          ELSQKT.PP..R..L....NTTVERRFSSWIGGSILASL
Retrocopy ELSQKT>PPPPRMRLKHTSNTTVERRFSSWIGGSILASL

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_1481 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009477	2 retrocopies	retro_chof_1481 , retro_chof_909,
Mus musculus	ENSMUSG00000027671	1 retrocopy	retro_mmus_1928,
Tursiops truncatus	ENSTTRG00000008907	1 retrocopy	retro_ttru_1431,