RetrogeneDB ID: retro_chof_679

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_134307:347..1047(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA8
• Ensembl ID: ENSCHOG00000004959
• Aliases: None
• Description: cell division cycle associated 8 [Source:HGNC Symbol;Acc:14629]

Sequence

>retro_chof_679
ATAGCTCCAGCTAGGAAAGGCAGCAGTTGGATAACCAAGACCAATTCTTTGAGGAGCCAGAAGCTTGCCTCCTTTCTCAA
GGACTTTGAGTTTGAAGTGCAAATCTGATCGAAGCAAATTCAGTCAGACAGGCAGAATCTTCTCAAGGAGATAGATAACC
TGTACAACATTGAGATCCTGTGGCTCTCCAAGGTGCTGCATGAGATGAACTGACTGGACTACTTTGCCCTTGGAGGAAAC
AAGCAGGCCTTGGAAGAGGTAGCAACAGCTGACCTAGATACCACAGAAATAAACAAACTAACTGCAGAAGCTATTCAGAC
TCCCCTGAAATCTGCCAAAACACAAAAAGCAATACAAGTGGTGAAATGATAGTGGAAGAAGAAGAAAATAAAAATATGAA
TAGTCAAACTGCAAGAGTCAGGTGTCCTCCAACCAAGAAGAGAACCCATTCCATACAAGGAAAAGGCAAAAACAAAAGGT
CAAGCCACTGGAACAGTGTTACCCCAGTTGTGGGCCAACTGGAGTTGTCTATGGTGAAACCAACTTCAGGCCTGACACCC
AGGTTTGATTCAAGGGTCTTCAAGACCCCAGGCCTGTGAACTCCAGCAGCCAAGAGCAGATTTACAATATCTCAATGAAT
GGCAGCCCCCTCACCAACAGCAAAGAGATTTTCCTTACTGTGCCAGTGGGAGGCAGAGAG

Alignment

ORF - retro_chof_679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 84.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPARKGGSRTTKTNSLRSRKLASFLKDFDREVQIRSKQIQSDRQNLLKEMDNLYNIEILRLPRALREMN
          .APARKG.S..TKTNSLRS.KLASFLKDF..EVQI.SKQIQSDRQNLLKE.DNLYNIEIL.L...L.EMN
Retrocopy IAPARKGSSWITKTNSLRSQKLASFLKDFEFEVQI*SKQIQSDRQNLLKEIDNLYNIEILWLSKVLHEMN

Parental  WLDYFALGGNKQALEEVATADLDITEINKLTAEAIQTPLKSAKTRKAIQV-DEMIVEEEEENKNTNPQTA
          .LDYFALGGNKQALEEVATADLD.TEINKLTAEAIQTPLKSAKT.KAIQV..EMIV.EEEENKN.N.QTA
Retrocopy *LDYFALGGNKQALEEVATADLDTTEINKLTAEAIQTPLKSAKTQKAIQV<GEMIV-EEEENKNMNSQTA

Parental  RVRRCPPAKKRTQSIQGKGKNKRSSRWNTVTPAVGRLELSMVKPTPGLTPRFDSRVFKTPGLRTPAAR-E
          RV.RCPP.KKRT.SIQGKGKNKRSS.WN.VTP.VG.LELSMVKPT.GLTPRFDSRVFKTPGL.TPAA..E
Retrocopy RV-RCPPTKKRTHSIQGKGKNKRSSHWNSVTPVVGQLELSMVKPTSGLTPRFDSRVFKTPGL*TPAAK<E

Parental  RIYNISMNGSPLANSKEIFLTVPVGGGE
          .IYNISMNGSPL.NSKEIFLTVPVGG.E
Retrocopy QIYNISMNGSPLTNSKEIFLTVPVGGRE

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_679 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.

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028556	2 retrocopies	retro_acar_139, retro_acar_200,
Choloepus hoffmanni	ENSCHOG00000004959	1 retrocopy	retro_chof_679 ,
Callithrix jacchus	ENSCJAG00000002008	1 retrocopy	retro_cjac_380,
Homo sapiens	ENSG00000134690	1 retrocopy	retro_hsap_4052,
Gorilla gorilla	ENSGGOG00000007719	2 retrocopies	retro_ggor_2594, retro_ggor_2721,
Microcebus murinus	ENSMICG00000011926	1 retrocopy	retro_mmur_1589,
Macaca mulatta	ENSMMUG00000014340	2 retrocopies	retro_mmul_1611, retro_mmul_2339,
Nomascus leucogenys	ENSNLEG00000011630	2 retrocopies	retro_nleu_2803, retro_nleu_3006,
Pongo abelii	ENSPPYG00000001526	2 retrocopies	retro_pabe_3224, retro_pabe_3234,
Pan troglodytes	ENSPTRG00000000552	3 retrocopies	retro_ptro_2531, retro_ptro_2533, retro_ptro_2746,