RetrogeneDB ID: retro_chof_888

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_162686:184..588(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000012770
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C11orf1
• Ensembl ID: ENSCHOG00000003039
• Aliases: None
• Description: chromosome 11 open reading frame 1 [Source:HGNC Symbol;Acc:1163]

Sequence

>retro_chof_888
AGACAGTCCCTCACTTACTTCCTGAGAAACCCACACTATGGCAGCTTCATTAATGCAGACGGCCATGCTGAAGTATGGAC
AGATTGGAATGATATGTCCAAGTTTTTCCAGTATGAATGGAGATGCACCACTAATGAGAATGCCTACTTGAACCATACTT
TGATGGGCAACTGGAACCAGGAAAGATATGACCTAAGGAATATCATGCAGTCAAAGCCCTTACCCACCCAGTATGGACAT
TACTTTGAAACAACATACAATGCAAGCTACAAAAAATGCCACTTTCAACCCATAGATGTAAGCGAGTGCCTCACTGGTTC
CCAGTACATAAACCTGAATTGGATCCTCCTCTTTACAAATGCACAGAAAAGTCAACTAATATGAATAGCTATTCAAAGCC
TCAA

Alignment

ORF - retro_chof_888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RHSLTYILRNPHCGSLINADGHAEV-TDWNDMSKFFQYGWRCTTNENAYSNHTLMGNWNQERYDLRNIMQ
          R.SLTY.LRNPH.GS.INADGHAEV.TDWNDMSKFFQY.WRCTTNENAY.NHTLMGNWNQERYDLRNIMQ
Retrocopy RQSLTYFLRNPHYGSFINADGHAEVWTDWNDMSKFFQYEWRCTTNENAYLNHTLMGNWNQERYDLRNIMQ

Parental  PKPLPSQFGHYFETTYDASY-NKMSLSTHRFKQEPHWFPGHQPELDPPQYKCTEKSTYMNSYSKPQ
          .KPLP.Q.GHYFETTY.ASY..KM.LSTHR.K..PHWFP.H.PELDPP.YKCTEKST.MNSYSKPQ
Retrocopy SKPLPTQYGHYFETTYNASY<QKMPLSTHRCKRVPHWFPVHKPELDPPLYKCTEKSTNMNSYSKPQ

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_888 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003039	3 retrocopies	retro_chof_1409, retro_chof_1629, retro_chof_888 ,
Cavia porcellus	ENSCPOG00000021163	1 retrocopy	retro_cpor_455,
Erinaceus europaeus	ENSEEUG00000009977	1 retrocopy	retro_eeur_658,
Mus musculus	ENSMUSG00000037971	1 retrocopy	retro_mmus_3061,