RetrogeneDB ID: retro_chof_52

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_92390:2197..3208(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000068
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013258
• Aliases: None
• Description: None

Sequence

>retro_chof_52
TCAGAGGAAGATGTTGAAAACCGGAATGTGTCCCATAATGAACACACACACCAAGAGATAAAGGGCCAAAAAACACTGGC
AACTCCTGCAGTTTGCTGCCTTGCAATGGAAAACAATATTAAGCTGAGTGAAGTTGTTGGCTCAGTAAAAGATGGCAGAA
TACTTAAGGAAGATATTCTCAACTATTTGGCGAAGCAGACAGGAGGTACATTATCTCCTTCACCAAAAGCCAAAATTATG
TCATCCCCAGCAACACCAAAAGACAGGACTATTCCTGTACCAATATCAAAATCTCTGGTATTCACAGGGAAAAACAGAAC
AGAACCCATTAAAGGCTTTCACAAAGCAATGGTCAAGACGATGACTACAGCCCTGAAGATTCCTCACTTTGGATACTGTG
ATGAGGTTGACCTTACTGAACTGGTTAAACTACGAGAAGAATTAAAGCCCATTGCTTTTGCTTATGGAATTAAACTCTCC
TTTATGCCCTTCTTAAAGTCTGCTTCCTTGAGATTACTACAGTTCCCCATTCTTAATGCTTCTGTGGATGAAAACTGCCA
GAACATAGCATATAAGGAATCTCATAAGATCGGGGTAATGATGGATACCGAGCAAGGGTTGTTTGTTCCTAATGTAAAAA
ATGTTCCGATCTGCTCTATATTTGAGACTGCTAGTGAAATGAACTGTCTCCAGAAATTGGGCTCTTCAGGTCAGATCAGA
ACCACTGATCTTACTACAGGAGGAACAATTACTCTTTCCAACATTGGATCAATTGGTGGTATCTATGCCAAACCGGTGAT
ATTGCCACCTGAAGTAGCAATTGGGGCTTTAAGATCAGTTAAGGCCCTTCCCCAATTTAACCAGAAGGGAGACATATATA
AGGCACAGATAATGAATGTGAACTGGTCAGCTGATCACAGAATTATTGATGGTGTTACAATGTCACACTTCTCTAATTTA
TGGAAATCCTACTTAGAAAAACGAGTTTTTATGTTACTGGATCTGAAATGA

Alignment

ORF - retro_chof_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.25 %
• Parental protein coverage: 69.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEEDVVETPAVSHDEHTHQEIKGQKTLATPAVRRLAMENNIKLSEVVGSGKDGRILKEDILNYLAKQTGA
          SEEDV.E...VSH.EHTHQEIKGQKTLATPAV..LAMENNIKLSEVVGS.KDGRILKEDILNYLAKQTG.
Retrocopy SEEDV-ENRNVSHNEHTHQEIKGQKTLATPAVCCLAMENNIKLSEVVGSVKDGRILKEDILNYLAKQTGG

Parental  ILPPSPKAEIMPPPATPKDRTIPLPVSKPPVFTGKDRTEPIKGFHKAMVKTMTAALKIPHFGYCDEVDLT
          .L.PSPKA.IM..PATPKDRTIP.P.SK..VFTGK.RTEPIKGFHKAMVKTMT.ALKIPHFGYCDEVDLT
Retrocopy TLSPSPKAKIMSSPATPKDRTIPVPISKSLVFTGKNRTEPIKGFHKAMVKTMTTALKIPHFGYCDEVDLT

Parental  ELVKLREELKPIAFSRGIKLSFMPFFLKAASLGLLQFPILNASVDENCQNITYKASHNIGVAMDTEQGLI
          ELVKLREELKPIAF..GIKLSFMP.FLK.ASL.LLQFPILNASVDENCQNI.YK.SH.IGV.MDTEQGL.
Retrocopy ELVKLREELKPIAFAYGIKLSFMP-FLKSASLRLLQFPILNASVDENCQNIAYKESHKIGVMMDTEQGLF

Parental  V-NIKNVQICSVFEIASELNRLQKLGSAGQIGTPDL-AGGTFTLSNVGSIGGTYTKPVILPPEVAIGALG
          V.N.KNV.ICS.FE.ASE.N.LQKLGS.GQI.T.DL..GGT.TLSN.GSIGG.Y.KPVILPPEVAIGAL.
Retrocopy VPNVKNVPICSIFETASEMNCLQKLGSSGQIRTTDLTTGGTITLSNIGSIGGIYAKPVILPPEVAIGALR

Parental  SIKALPRFNQKGEVYKAQIMNVSWSADHRVIDGATMSRFANLWKYYLENPAFMLLDLK
          S.KALP.FNQKG..YKAQIMNV.WSADHR.IDG.TMS.F.NLWK.YLE...FMLLDLK
Retrocopy SVKALPQFNQKGDIYKAQIMNVNWSADHRIIDGVTMSHFSNLWKSYLEKRVFMLLDLK

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_52 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003998	1 retrocopy	retro_chof_2128,
Choloepus hoffmanni	ENSCHOG00000013258	2 retrocopies	retro_chof_52 , retro_chof_655,
Microcebus murinus	ENSMICG00000006218	1 retrocopy	retro_mmur_1089,
Oryctolagus cuniculus	ENSOCUG00000014244	1 retrocopy	retro_ocun_952,
Otolemur garnettii	ENSOGAG00000005625	1 retrocopy	retro_ogar_2997,