RetrogeneDB ID: retro_chof_1493

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_30791:13044..14263(-)
• 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_1493
GACCCCCAAGATCAATGTAAGATATTTACCCAGGCATTTCACTTTTTAAAAAATAGTAAAAAAGCACAAATGACCACTGA
AAAACCAAAGCAAGATGCTATCAACATTCCCAAGAAACCTGTGCTGCTGGAATCTTATCATGGCCAAATTGTTCAGTCTA
AGGTTAATTCATTTAGAAAACCTCTACAAGTCAAATATGTGAGTTCTGCCACAACTCAGACACTTTCAACTGCTATCTCT
GAAACCACAGAGCCACAGCCTATAAACACAAGCAGTGTAACAGTGAAAAGTAATAGCACATCAAACAGAACTACCACAAA
ATTTGTGAGCCCTACATGTCAGGACATACAGCTTGGGTGACCTCCTATTAGAAGTCACCACAATAATAGCCAAGGCAAGG
TGAAACAGGGCATTGACAGAACTTCTGCCAGTGTTACAGTCCAGAAAGGGCCTACTGGAAAGTGATTACTACAGTTAAAA
ACAGATTTATCTACTGTCAAAATCAGTTCTTCTCAGGACACCAAAAGAAATGAGACATAATCAAGAAACCTGGCTTCTGA
AATTATAACCAAGCAGATTAATCTTCTAATACCAAACTTATAGAAAAGTCCAAAACCATTGACCAGCAAAGACATACTGT
AGCCCAAGCAGCCTTTGTTATATTGGCTCAGCCCAAAGAAACTGCAGAGGAGAGAAAAATCCATCTGACTGAGGGGAAAG
CTGGCAAAGAAAGAGTGCTGAAAAGGCCTCCTAGGTCTGTACTTACTCAACTAGAACCTGAAGGACAAAATGAAAACCCT
ATTGGGTCCTTCTGGACTACCATGTCAGAAGAAGATGAGCAGAGACTATTTACTGAAAAAGTAAACAAGACATTTTCTGA
ATGCCTGAATCTGATTAATGAGGGATGCCTCCCCAAAAAACAAATATTGGCCACACTGTATGACTTGGTTAAAAATATTC
CAAGCACTAAAATACTTGTTAAGTTTTGGATATACCTTGCAAGTCTTGGACCAATTACAAGTCCTATTGAAAATATTATC
ACAACCTATGAGAAAGTCATTCTGGCAGGGGCCCAGCCTACTGAAGAGGTGCAACATGCAATTGTAAATATTCTAACACT
GAAGAGTCAAGAAGTTAATTTTGGAGAAAGATTGAGGCTTGTGCAGCCACAGAACAAATTGAAGAAGTCAACACTGAAAA
TATAGGTGTTAATCTAGAT

Alignment

ORF - retro_chof_1493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.83 %
• Parental protein coverage: 59.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPQNQRMTFTQAFHLKKKSKDNQMTTEKLKQDAANIPKRPVLLGSYRGQIVQSKVNSFRKLLQVKDASSA
          .PQ.Q...FTQAFH..K.SK..QMTTEK.KQDA.NIPK.PVLL.SY.GQIVQSKVNSFRK.LQVK..SSA
Retrocopy DPQDQCKIFTQAFHFLKNSKKAQMTTEKPKQDAINIPKKPVLLESYHGQIVQSKVNSFRKPLQVKYVSSA

Parental  TTQKLSATVSEATEPQPVNTSSVTVKSNSNSNRATTKFVSTACQDRQLMRPPIRIHHSSNQDKVKQDISR
          TTQ.LS...SE.TEPQP.NTSSVTVKSNS.SNR.TTKFVS..CQD.QL..PPIR.HH...Q.KVKQ.I.R
Retrocopy TTQTLSTAISETTEPQPINTSSVTVKSNSTSNRTTTKFVSPTCQDIQLG*PPIRSHHNNSQGKVKQGIDR

Parental  TSARVTVQNGPTGKGLLQLKTDSSRVKISSSQDTKRNETSSRNLGSEIITRPAS-STNRKLIEKSKTIDQ
          TSA.VTVQ.GPTGK.LLQLKTD.S.VKISSSQDTKRNET.SRNL.SEIIT.....S.N.KLIEKSKTIDQ
Retrocopy TSASVTVQKGPTGK*LLQLKTDLSTVKISSSQDTKRNET*SRNLASEIITKQIN<SSNTKLIEKSKTIDQ

Parental  RRHTVAQATFVRSAQPKETAEERRIRLTEWKAGRGRVLKRPSSSVLTQLEPEGQNENPVGSFWTTMAEED
          .RHTVAQA.FV..AQPKETAEER.I.LTE.KAG..RVLKRP..SVLTQLEPEGQNENP.GSFWTTM.EED
Retrocopy QRHTVAQAAFVILAQPKETAEERKIHLTEGKAGKERVLKRPPRSVLTQLEPEGQNENPIGSFWTTMSEED

Parental  EQRLFTEKVNKIFSECLNLINEGC-PKEEVLATLNDLVKNIPDAKKLVKYWICLARLEPITSSIENIITI
          EQRLFTEKVNK.FSECLNLINEGC.PK...LATL.DLVKNIP..K.LVK.WI.LA.L.PITS.IENIIT.
Retrocopy EQRLFTEKVNKTFSECLNLINEGCLPKKQILATLYDLVKNIPSTKILVKFWIYLASLGPITSPIENIITT

Parental  YEKAILAGAXPIEEMRHAIVDILTLKSQEELNFGE-KTKACAATEEIQEVNTDNIGVNLE
          YEK.ILAGA.P.EE..HAIV.ILTLKSQ.E.NFGE.K..ACAATE.I.EVNT.NIGVNL.
Retrocopy YEKVILAGAQPTEEVQHAIVNILTLKSQ-EVNFGE<KIEACAATEQIEEVNTENIGVNLD

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_1493 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,