RetrogeneDB ID: retro_chof_973

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_17823:416..1665(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2
• Ensembl ID: ENSCHOG00000009905
• Aliases: None
• Description: cytoskeleton associated protein 2 [Source:HGNC Symbol;Acc:1990]

Sequence

>retro_chof_973
TTAGAAAGGAAAATATGTTTTTTATGCAAAGAGGAAGATCAGACATTATCCAGTAGAAACCGGAGAATGATGACATCTGA
ACACTGCTAGGTCCAAGAAGGGACAAAAGTTCTGAACCTTAAAACTAATATGGCTGGTAAAGAAAATGCCAATAGACCTA
TAGAGACCAAAAAAATATATATATACAAGGATGGGGAAAATTGTATTCTTTAAAACCTTCTAATGAATTAATCAATTCAA
ATAGAGTACTTGATATACATAATTTAGAAGATAATAATCAAACTATTCAGTTATTACCAATTAAAGATGATCCCCAAATT
CAACATAGGATATTTAGCCAGGGATTTCACTTAAAAAAAAATAGTAAAGAAAACCAAATGACCACAGAAAAGGCAAAACA
AGATGCTACTAACATTCCCAAGAAACCTGTGCTTGGATCTTATCATGGCCAAATTGTTCAGTCTAAGGTTAATTCATTTA
GAAAACCTCAGAGAGTCTAAGATATGAGTTCTGCCACAACCAAGAAACTTTCAACTACTGTCTCTGAAGCCACAGAGCCT
CAGCCTGTAGACAGCAGCAGTGTAACAATGAAGAGTAATAGAGCTTCGGACAGAACTACCGCAGAATGTGTGACCACAAC
ATGTCAGTACAGACAGCTTGTGCGACCTTCTATTAGAAGTCACCACAATAACAGCCAGGACAAGGTGAAAAAGGGCATCA
GCAGAACATCTGCTAATGTTACAGTCCAGAAAGGGCCCACTGGAAAGGGATTGCTATGATTTAAAACAGATTTATCTACT
GTCAAAATCAGTTCTTCTTAAGACACGTAAAGAAATGAGACATCATCAAGAAACATGGCTTCTGAAATTATAACCAGGCC
ACCTTCGTCTTTTAATAACAAACTGATAGAAAAGCCCAAAACCACTGACCAGCAAAGGTGTATCACAACCTTTGTTAGAT
CAGCTCAGCCCAAAGAAACTGCAGAAAAGAGAAAAATCCATTTGACTGAGTGGAAAGCTGGCCAAGGAAGAGTGTTGAAA
AGGCCTCTTTGCTCTGTACTTACCAGCTAGAACCTGAAGGATAAAATGAAAACCCTGTTGGGTGTTTTTGGACTACCATG
AGAGAAGAAGATGAGCAGAGACTATTTACTGAAAAAGTAAATATGATATTTTTTGAGTGCCTGAACCTGATTAATGACGG
ATGCCCAAAAGAAGAAATATTGGCCCCCCTGAATGACCTGGTTAACAAT

Alignment

ORF - retro_chof_973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.28 %
• Parental protein coverage: 61.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEGKTRFVYKEKDQILSSSKDRRMMTSEHQ-VQERTKVLKLKTKMADKENANRPTESKNIMTEK---NCI
          LE.K..F..KE.DQ.LSS...RRMMTSEH..VQE.TKVL.LKT.MA.KENANRP.E.K.I...K...NCI
Retrocopy LERKICFLCKEEDQTLSS-RNRRMMTSEHC*VQEGTKVLNLKTNMAGKENANRPIETKKIYIYKDGENCI

Parental  -PLQPSNDLTSLTIAVDTYNFEDNNQMLQLLPIEGEPQNQRMTFTQAFHLKKKSKDNQMTTEKLKQDAAN
          ..L.PSN.L.......D..N.EDNNQ..QLLPI...PQ.Q...F.Q.FH....SK.NQMTTEK.KQDA.N
Retrocopy <SLKPSNELINSNRVLDIHNLEDNNQTIQLLPIKDDPQIQHRIFSQGFHXXXXSKENQMTTEKAKQDATN

Parental  IPKRPVLLGSYRGQIVQSKVNSFRKLLQVKDASSATTQKLSATVSEATEPQPVNTSSVTVKSNSNSNRAT
          IPK.PVL.GSY.GQIVQSKVNSFRK...V.D.SSATT.KLS.TVSEATEPQPV..SSVT.KSN..S.R.T
Retrocopy IPKKPVL-GSYHGQIVQSKVNSFRKPQRV*DMSSATTKKLSTTVSEATEPQPVDSSSVTMKSNRASDRTT

Parental  TKFVSTACQDRQLMRPPIRIHHSSNQDKVKQDISRTSARVTVQNGPTGKGLLQLKTDSSRVKISSSQDTK
          ...V.T.CQ.RQL.RP.IR.HH...QDKVK..ISRTSA.VTVQ.GPTGKGLL..KTD.S.VKISSS.DT.
Retrocopy AECVTTTCQYRQLVRPSIRSHHNNSQDKVKKGISRTSANVTVQKGPTGKGLL*FKTDLSTVKISSS*DT*

Parental  RNETSSRNLGSEIITRPASSTNRKLIEKSKTIDQRRHTVAQATFVRSAQPKETAEERRIRLTEWKAGRGR
          RNETSSRN..SEIITRP.SS.N.KLIEK.KT.DQ.R......TFVRSAQPKETAE.R.I.LTEWKAG.GR
Retrocopy RNETSSRNMASEIITRPPSSFNNKLIEKPKTTDQQR---CITTFVRSAQPKETAEKRKIHLTEWKAGQGR

Parental  VLKRPSSSVLT-QLEPEGQNENPVGSFWTTMAEEDEQRLFTEKVNKIFSECLNLINEGCPKEEVLATLND
          VLKRP..SVLT.QLEPEG.NENPVG.FWTTM.EEDEQRLFTEKVN.IF.ECLNLIN.GCPKEE.LA.LND
Retrocopy VLKRPLCSVLT<QLEPEG*NENPVGCFWTTMREEDEQRLFTEKVNMIFFECLNLINDGCPKEEILAPLND

Parental  LVKN
          LV.N
Retrocopy LVNN

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_973 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Choloepus hoffmanni	ENSCHOG00000009905	2 retrocopies	retro_chof_1493, retro_chof_973 ,
Cavia porcellus	ENSCPOG00000012382	1 retrocopy	retro_cpor_171,
Felis catus	ENSFCAG00000010021	1 retrocopy	retro_fcat_1770,
Myotis lucifugus	ENSMLUG00000000132	1 retrocopy	retro_mluc_1515,
Monodelphis domestica	ENSMODG00000010436	1 retrocopy	retro_mdom_1364,
Mustela putorius furo	ENSMPUG00000017996	1 retrocopy	retro_mputfur_1270,
Mus musculus	ENSMUSG00000037725	1 retrocopy	retro_mmus_2651,
Otolemur garnettii	ENSOGAG00000008428	1 retrocopy	retro_ogar_1743,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176,
Tursiops truncatus	ENSTTRG00000009624	2 retrocopies	retro_ttru_1491, retro_ttru_1741,