RetrogeneDB ID: retro_chof_1788

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_384462:179..986(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIOK3
• Ensembl ID: ENSCHOG00000008343
• Aliases: None
• Description: RIO kinase 3 [Source:HGNC Symbol;Acc:11451]

Sequence

>retro_chof_1788
ATGGATCTGGTCAGAGTGGCATCACTTGAGCCCCGCTCCACAGCGGCCTGGGGACTCAGCAAGTGTCCATGGGCTATCCC
TCAAAATACAAGATCTTGTTCCTTGGCTGACATATTGATGAACTGTTGACTAAAGAAATGCAATTAGAAGAAGAAGCTGC
TGCTTTTCCTGAAGTTGCTATTGCTAAAGGACCATTTATTACTGGAGAAATCACTGACACCTACAGGGACCTGCTGGCTC
AGATGTCACAGATGGAATTTGATGGAGAATATGATGCACAGCTTAGGCGTAAAGAAAAAAATTCAATGGAGATAGCAAAG
CTTGCATTTCCTTTGAAAATTATCAAAAAGTGCATCCTTATGAATACAGTGACAGCTCTGAAGATAAGGTTGACTAGAAG
GATACTCATGACGATCCCTACATCCCAGCAAAACCAATTCCTACTCCCCAAAAGTATTTATTGGAAAAGGGAAAGACATC
ACCACCAAACATGATGAAGTTGTATGTGGGAGAAAGAATATAGCGAGAATGGAAAATTTTGCACCTGGGTTTCAGGTAGG
AGATGGAATTTGAATGTATTTAAAACAATCAAACCAATGTTTTCAATTGTTTAAAACAGCATGCCCATTCAGAAGACCGT
CAAAGTGCCCACCTCCGTGAGAAAAAGGAGCATTCTATCATGGAAAAAGCAGTTGATCCTAAGACCCATTTACTTATGTA
TAAAATGATCAACTCTGGAATGTCGGAGACAATCACTGCTGTATTAGAACAGGAAAGGAATCTGTTGTCTGTCATGCATA
TGGAGGG

Alignment

ORF - retro_chof_1788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.9 %
• Parental protein coverage: 52.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MDLVGVASPEPGPAAAWGPSKWPWATPQNTISCSLADVM-SEQLAKELQLEEEAAAFPEVVVAEGPFITG
          MDLV.VAS.EP...AAWG.SK.PWA.PQNT.SCSLAD....E.L.KE.QLEEEAAAFPEV..A.GPFITG
Retrocopy MDLVRVASLEPRSTAAWGLSKCPWAIPQNTRSCSLADIL<DELLTKEMQLEEEAAAFPEVAIAKGPFITG

Parental  ENIDTSSDLMLAQMLQMEFDREYDAQLRREEK-KFNGDSKVSISFENYRKVHPYEDSDSSEDEVDWQDTR
          E..DT..DL.LAQM.QMEFD.EYDAQLRR.EK.KFNGDSK..ISFENY.KVHPYE.SDSSED.VD..DT.
Retrocopy EITDTYRDL-LAQMSQMEFDGEYDAQLRRKEK<KFNGDSKACISFENYQKVHPYEYSDSSEDKVD*KDTH

Parental  DDPYIPAKPVPTPK-KGFIGKGKDITTKHDEIVCGRKNTARMENFAPGFQVGDGIGMDLKLSN-HVFNAL
          DDPYIPAKP.PTP..K.FIGKGKDITTKHDE.VCGRKN.ARMENFAPGFQVGDGI.M.LK.SN..VFN.L
Retrocopy DDPYIPAKPIPTPQ<KVFIGKGKDITTKHDEVVCGRKNIARMENFAPGFQVGDGI*MYLKQSN>NVFNCL

Parental  KQHAYSEERRSARLHEKKEHSTAEKAVDPKTRLLMYKMINSGMLETITG-CISTGKESVVFHAYGG
          KQHA.SE.R.SA.L.EKKEHS..EKAVDPKT.LLMYKMINSGM.ETIT..CI.TGKESVV.HAYGG
Retrocopy KQHAHSEDRQSAHLREKKEHSIMEKAVDPKTHLLMYKMINSGMSETITA<CIRTGKESVVCHAYGG

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_1788 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008343	1 retrocopy	retro_chof_1788 ,
Callithrix jacchus	ENSCJAG00000020556	1 retrocopy	retro_cjac_2617,
Echinops telfairi	ENSETEG00000003689	1 retrocopy	retro_etel_2181,
Macropus eugenii	ENSMEUG00000006292	1 retrocopy	retro_meug_1278,
Macaca mulatta	ENSMMUG00000021478	1 retrocopy	retro_mmul_1291,
Ochotona princeps	ENSOPRG00000004803	2 retrocopies	retro_opri_1034, retro_opri_946,
Pongo abelii	ENSPPYG00000009062	1 retrocopy	retro_pabe_1011,