RetrogeneDB ID: retro_chof_1832

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_399026:9..567(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNDBP1
• Ensembl ID: ENSCHOG00000012594
• Aliases: None
• Description: cyclin D-type binding-protein 1 [Source:HGNC Symbol;Acc:1587]

Sequence

>retro_chof_1832
GGCGAAGCCCGGAAGACCACAGAGGAGTTTAATCGGGAGAAGTTTTGGAAAAGACTCAATGACGCAGCTGTGAATGTGTC
AAGGGAAGCCACGAATCTGACCGTCTTCTCTTGACTTCCACTGTCGTCTCCACAGAAAACTCAGATGTGCTGTGAGAAAG
TCCATGCTGCCATTGAGGCAATTACTGCAGTGTACTATTCACTTCCCAAGGATCAGGGAATCACTCTACGAAAGCTGGTA
CGGAGTGCTACTCTGGATATTGTGGATGGCATGGCCCAGCTTTTGGAAGTGCTTTCTATCACTCCAGCTCAAAGCCCAGA
GAACAAGGATCTTATTTCCTGCAGCAGTGTCTGGGTTGCATGGGAACAGATGCCTCAGACACCAAGAGATAACAAAGCTG
CAGCCCTTTTAATGCTGACAAAGAGTGTGAATTTTGTGAAAGATGCACTAGAGGAAATGGAGTGCACTGTGGAAGAATGT
GACCCTTACTCTGGCCTCTTGAATGACTCTGAGGAGGACAACTCTGATAATCCTGATAATGAGAATTCCACCACATTG

Alignment

ORF - retro_chof_1832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.48 %
• Parental protein coverage: 53.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GEARETTEEFNREKFWKRLNDAAENVSREATNLTVFSRLPLSSPQKTQMCCEKVHAAIEAITAVYYSLPK
          GEAR.TTEEFNREKFWKRLNDAA.NVSREATNLTVFS.LPLSSPQKTQMCCEKVHAAIEAITAVYYSLPK
Retrocopy GEARKTTEEFNREKFWKRLNDAAVNVSREATNLTVFS*LPLSSPQKTQMCCEKVHAAIEAITAVYYSLPK

Parental  DQGITLRKLVRSATLDIVDGMAQLLEVLSITPAQSPENKDLISCSXXXXXXXXXXXXXXXNRAAALLMLT
          DQGITLRKLVRSATLDIVDGMAQLLEVLSITPAQSPENKDLISCS...............N.AAALLMLT
Retrocopy DQGITLRKLVRSATLDIVDGMAQLLEVLSITPAQSPENKDLISCSSVWVAWEQMPQTPRDNKAAALLMLT

Parental  KSVNFVKDALEEMERAVEECDPFSGLLNDSEEDNSDNLDNEEEDVL
          KSVNFVKDALEEME..VEECDP.SGLLNDSEEDNSDN.DNE....L
Retrocopy KSVNFVKDALEEMECTVEECDPYSGLLNDSEEDNSDNPDNENSTTL

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_1832 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	ENSCHOG00000012594	2 retrocopies	retro_chof_1251, retro_chof_1832 ,
Loxodonta africana	ENSLAFG00000004497	1 retrocopy	retro_lafr_680,
Otolemur garnettii	ENSOGAG00000011162	1 retrocopy	retro_ogar_1358,