RetrogeneDB ID: retro_chof_1442

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_29548:457..1025(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000002579
• Aliases: None
• Description: None

Sequence

>retro_chof_1442
ATGAAGTTGTCAGTCAGATGTGGCAAAGCCCAGCTTGTCATGCCAGTCTGGTTTCTGGACAGATTCCAGCAGACGGCAGC
TTCCACCGTTTCTTTCTCTGAAATAGACCATCCATACATCTTAATTACAGGAGGTCTTGGTCAGCGTGGAGTAGGGCTTA
CTAACTTTTTGGAGGAAACGATTTGAAAAAGCACAATGCAATCTTTAAGACATAAGGAAACTCCTCCATTCACATCTTCC
AGAGTGGGGAATTTATTTATTCTGACATTTTGGATTACAAAAATCTTTGTAGTATAGTGGTAAACAACTGCATCACTTGA
CTGTTTCATTGAAGTGACTCCCTCAGCATGGTTGGAGAAACAAATGTATCCTGGGTGAGAACTGTGAATACAACTGTATT
ACCTAATGTTCTGGATGTTGCTGCAGAACAAAATTTGCGATTGTTTGTGCCTGGCACCATTGGAGACTCTGGATCTACTT
CTCCCTGGAATCCAACCCACTATCTCTGTGTTCAAAGACCCAGGACCATTTATGGTATGTCCAAGTCCATGCCAAACTCA
AGGGAGAA

Alignment

ORF - retro_chof_1442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.97 %
• Parental protein coverage: 81.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQQSPACGCWLSAVPARFLGTLPRQVQSDASFHSVSFSEIDHPRILITGGLGQLGVGLANFL-RKRFGKQ
          M..S..CG......P..F...L.R..Q..AS...VSFSEIDHP.ILITGGLGQ.GVGL.NFL.RKRF.K.
Retrocopy MKLSVRCGKAQLVMPVWF---LDRFQQTAAS--TVSFSEIDHPYILITGGLGQRGVGLTNFL>RKRFEKA

Parental  NVILSDIRKPPN-HIFQSGPFIYSDILDYKHLREVVVNNRITWLFHYSALLSAVGETNVSLARAVNITGL
          ...L.DIRK....HIFQSG.FIYSDILDYK.L...VVNN.IT.LFH.S..LS.VGETNVS..R.VN.T.L
Retrocopy QCNL*DIRKLLH>HIFQSGEFIYSDILDYKNLCSIVVNNCIT*LFH*SDSLSMVGETNVSWVRTVNTTVL

Parental  HNVLDVAAEHSLRLFVPSSIGAFGPTSPRNPTPDLCIQRPRTIYGVSK-VHAELMGE
          .NVLDVAAE..LRLFVP..IG..G.TSP.NPT..LC.QRPRTIYG.SK.VHA.L.GE
Retrocopy PNVLDVAAEQNLRLFVPGTIGDSGSTSPWNPTHYLCVQRPRTIYGMSK<VHAKLKGE

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_1442 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002579	1 retrocopy	retro_chof_1442 ,
Callithrix jacchus	ENSCJAG00000004107	1 retrocopy	retro_cjac_3935,
Mus musculus	ENSMUSG00000021953	1 retrocopy	retro_mmus_1962,