RetrogeneDB ID: retro_chof_1854

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_403614:241..565(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf57
• Ensembl ID: ENSCHOG00000011410
• Aliases: None
• Description: chromosome 6 open reading frame 57 [Source:HGNC Symbol;Acc:20957]

Sequence

>retro_chof_1854
ATGACCACCTTGGGCCTTGCAGGGCTGCTCAACCATGTTCCAGTCACAGTGTAGAGAATGGCAAGATCACCCCTTTTGTG
CCATTCTTTGAAGAAAACGAGTTCTTCTCTAGGACGAAAGTCTGAACCTGCCAAATAATTCCTTAAGAAGCCAAAGCTAT
CAGAAGGTTGTTTTGATGTACCAGAAGGTTCCCATTTAGAGAAAGAACCACTGGAAAAATTTCCTCATGATTTTAATCCT
GTTCCCAAAGAAAAGGGTGGACCCAGGGACCCAGAACCTACTCAGTACAGAGATTGGGAATGTAAAGGACGTTAATTGAC
TTTT

Alignment

ORF - retro_chof_1854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTLGLAGRLNRVPARAWRTARSPLLWHSLRKTSS-LGGKSEPAKQSLKKPKLPEGRFDVPEGSHLEKEP
          MTTLGLAG.LN.VP....R.ARSPLL.HSL.KTSS.LG.KSEPAK..LKKPKL.EG.FDVPEGSHLEKEP
Retrocopy MTTLGLAGLLNHVPVTV*RMARSPLLCHSLKKTSSSLGRKSEPAK*FLKKPKLSEGCFDVPEGSHLEKEP

Parental  LEKFPDDVNPVTKEKGGPRGPEPTRYGDWERKGRCIDF
          LEKFP.D.NPV.KEKGGPR.PEPT.Y.DWE.KGR...F
Retrocopy LEKFPHDFNPVPKEKGGPRDPEPTQYRDWECKGR*LTF

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_1854 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002602	2 retrocopies	retro_cfam_268, retro_cfam_657,
Choloepus hoffmanni	ENSCHOG00000011410	6 retrocopies	retro_chof_176, retro_chof_1854 , retro_chof_252, retro_chof_465, retro_chof_694, retro_chof_966,
Erinaceus europaeus	ENSEEUG00000011260	1 retrocopy	retro_eeur_539,
Echinops telfairi	ENSETEG00000011154	1 retrocopy	retro_etel_1362,
Felis catus	ENSFCAG00000026799	1 retrocopy	retro_fcat_986,
Rattus norvegicus	ENSRNOG00000028087	1 retrocopy	retro_rnor_1514,
Tupaia belangeri	ENSTBEG00000004344	2 retrocopies	retro_tbel_3788, retro_tbel_4408,
Tarsius syrichta	ENSTSYG00000001769	1 retrocopy	retro_tsyr_67,