RetrogeneDB ID: retro_chof_1918

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_422296:411..721(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDSP2
• Ensembl ID: ENSCHOG00000005618
• Aliases: None
• Description: CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 [Source:HGNC Symbol;Acc:17077]

Sequence

>retro_chof_1918
CCAACCAACAATGCTGGCTTCATAGAGCCTATAGAGATTGAGGGGACCTCTCACTAGGTATATGTGTGCAAGAGGCCATA
TGTGGATTAATTCCTGAGAAGATTGGGAGAACGCTTTGAATGTGTCCTCTTCACTGCCAATCTGGCTAAGTATGCTGACC
TATGATGGATCTGCTAGACTAGTGGGGGGTATCCAGGATTGCCTATTTTGGGAGTCCTGTGTGTTCCACCAGGGCTTCTA
TGTAAAGAAGCTCAGTCACTTGGGGAGGAACCTGGGGAAAACCTTCATCCTGAACAACTTGCCTGCCTCT

Alignment

ORF - retro_chof_1918 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 63.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PINNADFIVPVEIEGTTHQVYVLKRLYVDEFMRRMGELFECVLFTASLAKYAD-PVTDLLDRCGVFRAR-
          P.NNA.FI.P.EIEGT.H.VYV.KR.YVD.F.RR.GE.FECVLFTA.LAKYAD.P..DLLD..GV.R...
Retrocopy PTNNAGFIEPIEIEGTSH*VYVCKRPYVD*FLRRLGERFECVLFTANLAKYAD<PMMDLLD*WGVSRIA<

Parental  LFRESCVFHQGCYVKDLSRLGRDLRKTLILDNSPAS
          LF.ESCVFHQG.YVK.LS.LGR.L.KT.IL.N.PAS
Retrocopy LFWESCVFHQGFYVKKLSHLGRNLGKTFILNNLPAS

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_1918 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005618	1 retrocopy	retro_chof_1918 ,
Callithrix jacchus	ENSCJAG00000006503	2 retrocopies	retro_cjac_3087, retro_cjac_919,
Petromyzon marinus	ENSPMAG00000009544	2 retrocopies	retro_pmar_20, retro_pmar_27,