RetrogeneDB ID: retro_chof_2340

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_67136:3821..4261(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000005213
• Aliases: None
• Description: None

Sequence

>retro_chof_2340
CAAGTGTCTCCTTTGGTCAGTGTGACATCATTCAGACACTTCTACAGAGGTGACAGCCCAGCAGATTCTCAAAAAGACAT
TGTTGAAATCCCCTTGCCTCCATGGCAGGAGTGAAACTGATGAGTCCATCAAAACCAAAAAGAGCTAGTCTACTCTATGA
AAACAGGAAGAGGGGAATGTTGGAAAACTGCATTCTCCTTAGCCTCTTTGCTAAAGAATATCTGTACCAAATGACAGAGA
AACAACTGAACCTCTGTGATCACCTGATTACTGAGCCTAGTAACGACTGGGATATTTATTACTGGGCCACAGAAGCAAAA
CCAGCCCCAGAAATATTTGAAAAGGAATCCCTGACACTGCTGAGAGACTTTACCAAGAACAAAAACAAAGAGTAGAGGCT
GAGTACCCCAGATCTCGAATACCTCTTTGAAAAGCCACGT

Alignment

ORF - retro_chof_2340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.81 %
• Parental protein coverage: 87.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QVSPLVSVTSFRRFYRGDSPADSQKDMIEIPLPPWQE-RTDESLETK-RARLLYESRKRGMLENCILLSL
          QVSPLVSVTSFR.FYRGDSPADSQKD..EIPLPPWQE..TDES..TK.RA.LLYE.RKRGMLENCILLSL
Retrocopy QVSPLVSVTSFRHFYRGDSPADSQKDIVEIPLPPWQE>ETDESIKTK>RASLLYENRKRGMLENCILLSL

Parental  FAKEYLHEMTEKQLNLYDRLINEPSNDWDIYYWATEAKPAPEVFENEILTLLRDFTKNKNKEQRLRAPDL
          FAKEYL..MTEKQLNL.D.LI.EPSNDWDIYYWATEAKPAPE.FE.E.LTLLRDFTKNKNKE.RL..PDL
Retrocopy FAKEYLYQMTEKQLNLCDHLITEPSNDWDIYYWATEAKPAPEIFEKESLTLLRDFTKNKNKE*RLSTPDL

Parental  EYLFEKPR
          EYLFEKPR
Retrocopy EYLFEKPR

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_2340 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005213	2 retrocopies	retro_chof_2032, retro_chof_2340 ,
Monodelphis domestica	ENSMODG00000020366	1 retrocopy	retro_mdom_1118,