RetrogeneDB ID: retro_chof_224

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_4961:13775..14160(-)
• Located in intron of: ENSCHOG00000005203

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000007947
• Aliases: None
• Description: None

Sequence

>retro_chof_224
TTCAAGAGGTTTGATAAATCAAATATGACATTGATAAGTGGACAAAGAAGATAGTGAGAATCTAGCTGACACCTGTGCTG
TTCTGCACATGAAGAGAGGTGACTGGAAAAAAGGAAACTGAACAACTTCTGTGGAAGGAGCATTTTGTAAAGTAGCTATT
CCATATCAAAAGAGATATTTATTAGACAACCACATCTTAATTTCAGTTTTGGTGATTGCTAGTACAGTAATTTTGACAGT
TTGGGGAGCAATGGTTTGGTTCCTGTACAAAAGAAATTCAGATTCTGGCTTCACCACAGTTTTTTCAACTGCACCTCAAT
TACCTTGTAACGATGACAGTGTCTTGGTAGCTGCAGAAGAAAATGAATATGCTGTTCAATTTGAC

Alignment

ORF - retro_chof_224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.21 %
• Parental protein coverage: 56.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FKWSDKSNMTFV-KWAD-QDGETLVDTCAFLQMKTGEWKKGNCELSSVEGTLCKAVIPYQKKYLSDNHIL
          FK..DKSNMT...KW....D.E.L.DTCA.L.MK.G.WKKGN....SVEG..CK..IPYQK.YL.DNHIL
Retrocopy FKRFDKSNMTLI<KWTK<EDSENLADTCAVLHMKRGDWKKGN*T-TSVEGAFCKVAIPYQKRYLLDNHIL

Parental  ISALVIASTLILTVLGAVIWFLYKRSADSGFTTVFSAAPQSPYNDDCVLVVAEENEYAVQFD
          IS.LVIAST.ILTV.GA..WFLYKR..DSGFTTVFS.APQ.P.NDD.VLV.AEENEYAVQFD
Retrocopy ISVLVIASTVILTVWGAMVWFLYKRNSDSGFTTVFSTAPQLPCNDDSVLVAAEENEYAVQFD

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_224 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	ENSCHOG00000007947	2 retrocopies	retro_chof_224 , retro_chof_2460,
Oryctolagus cuniculus	ENSOCUG00000016361	1 retrocopy	retro_ocun_927,
Tarsius syrichta	ENSTSYG00000002564	1 retrocopy	retro_tsyr_71,