RetrogeneDB ID: retro_chof_1102

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_200348:3474..4368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK8
• Ensembl ID: ENSCHOG00000001443
• Aliases: None
• Description: cyclin-dependent kinase 8 [Source:HGNC Symbol;Acc:1779]

Sequence

>retro_chof_1102
GGAAGAGTAAAAATTGCTGACATGGGCTTTGCCCGATTATTTAATTCACCTTTGAAGCCTTTAGCAGATTTGGATCCAGT
AGTGGTAACATTCTGGTACCAAGCCCCAGAATTGCTTCTTGGAGCAAGGCATTATACCAAAGCTATTGATATTTGGGCTA
TAGGGTATATATTTGCAGAACTACTAACGTCAGAACCAATATTTCACTGTCGACAAGAGGACATCAAAACTAGTAATCCT
TATCACCATGACCAGCTGGACAGAATATTCAATGTAATGGGATTTCCTGCAGATAAAGATTGGGAAGATATAAAAAAGAT
GCCTGAGCATTCAACATTAATGAAAGATTTCAGAAGAAATACGTACACCAACTGCAGCCTTATTAAGTATATGGAAAAAC
ATAAAGTTAAACCAGATAGCAAAGCATTCCACTTGCTTCAGAAGTTGCTTACCATGGACCCAATAAAGCGAATTACCTCA
GAACAGACTATGCAGGATCCCTATTTCTTAGAAGACCCACTTCCTACATCAGACGTTTTTGCCGGTTGTCAAATTCCTTA
CCCAAAACGAGAATTTTTAACAGAAGAAGAACCTGATGACAAAGGAGACAAAAAGAACCAGCAGCAACAGCAGGGCAATA
ACCATACTAATGGAACTGGTCACCCAGGGAATCAAGACAGCAGTCACACGCAGGGACCCCCGTTGAAAAAAGTGAGAGTT
GTTCCTCCTACCACTACCTCAGGTGGACTCATCATGACCTCAGACTATCAGCGTTCCAATCCACATGCTGCCTATCCCAA
CCCTGGACCAAGCACATCACAGCCACAGAGCAGCATGGGATATTCAACTACCTCCCAGCAGCCACCACAGTACTCACATC
AGACACATCAGTAC

Alignment

ORF - retro_chof_1102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.99 %
• Parental protein coverage: 64.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRVKIADMGFARLFNSPLKPLANLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHC
          GRVKIADMGFARLFNSPLKPLA.LDPVVVTFWY.APELLLGARHYTKAIDIWAIG.IFAELLTSEPIFHC
Retrocopy GRVKIADMGFARLFNSPLKPLADLDPVVVTFWYQAPELLLGARHYTKAIDIWAIGYIFAELLTSEPIFHC

Parental  -QEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDS
          .QEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDS
Retrocopy RQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDS

Parental  KAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQ
          KAFHLLQKLLTMDPIKRITSEQ.MQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQ
Retrocopy KAFHLLQKLLTMDPIKRITSEQTMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQ

Parental  QGNNHTNGTGHPGNQDSSHTQGPPLKKVRVVPPTTTSGGLIMTSDYQRSNPHAAYPNPGPSTSQPQSSMG
          QGNNHTNGTGHPGNQDSSHTQGPPLKKVRVVPPTTTSGGLIMTSDYQRSNPHAAYPNPGPSTSQPQSSMG
Retrocopy QGNNHTNGTGHPGNQDSSHTQGPPLKKVRVVPPTTTSGGLIMTSDYQRSNPHAAYPNPGPSTSQPQSSMG

Parental  YSTTSQQPPQYSHQTHRY
          YSTTSQQPPQYSHQTH.Y
Retrocopy YSTTSQQPPQYSHQTHQY

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_1102 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001443	1 retrocopy	retro_chof_1102 ,
Homo sapiens	ENSG00000132964	1 retrocopy	retro_hsap_2147,
Myotis lucifugus	ENSMLUG00000009176	1 retrocopy	retro_mluc_112,
Macaca mulatta	ENSMMUG00000014841	1 retrocopy	retro_mmul_1010,
Mus musculus	ENSMUSG00000029635	1 retrocopy	retro_mmus_1200,
Nomascus leucogenys	ENSNLEG00000014010	1 retrocopy	retro_nleu_2746,