RetrogeneDB ID: retro_cfam_858

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:5345472..5346651(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2L
• Ensembl ID: ENSCAFG00000007242
• Aliases: None
• Description: cytoskeleton associated protein 2-like [Source:HGNC Symbol;Acc:26877]

Sequence

>retro_cfam_858
GCTCCAAGATCAAATACCAAGTGCCAAAATGCCAAGCCCTTATGTAAAAGCTAAAAGTAATTGTCTGAATCTTCTACCTT
TTGAATCTATTATTATGCCCAAAAAGGATGTTACCAATCATATTAATTTGCCTATCAAAGCTATAAGATCCATCAGCATT
AAACCCCAGCCCAGACCTACCAATATCACAGGATCCAGAAACCAAAGTTGGAGACACCAAAACTTCCAGGCAAAAGACAG
ACTTAAGGATGAATTTCTTCTAACTTAAATCGTCAGCCTTCCAGCAATAGTCAACAACAGCATGAAACTGGATCCTCCAC
TACTGAAGAAGTGTCTAGAAAAACTGTGGGGTCACTTAATATATAGCCCCGAAAACTGCAAAGAAGCAGGTGGCAGATCA
AGGAAATGTTAAATGTGCAGACTCTGTGGACAATAACCATGTTGAAAATGAATCATTGAATACTTTCTAAAAGAGATAAA
CACAAAGAGACTTGCCTAAAACTTTCCCAGACTGAAAGGAAGCCAAATCCTGAATTACAGACAATAGGTAAACCAAAGAT
TATCTCTTATAATCAAACCAAGAGCAGTTTGGCTCCTAAATAAGCCTTGGGCAAAATTTCAGGGAATAGTGCTATTCTGA
AAGACAGAGTTAATAAAGAATTTGTTAGGGAACCACAAATTAGGATTCCACCACAAAAGCCACAGCAACTTTTGAGAGGA
ACAAATCTTGCAAGAACAGGAGAAAAATTCTCAAAGACAGTTCTTTCTCATTATGTTCAACCCCTTAGTAGGACTCTAAA
ATCAAAGAAACCAGTCATCAAGGACATAAAGGTTAATGGAGATAAATACAAAAGACCAAATGAAATTAAGTTACAGTCAC
ACACTGCTACTGAACAAAATATAAAGCAATCCAAACCCTGGACATGCCCCAGTGTGTTTCAGGGAGGCTATAGCAACAGA
CATTCAAACAAGAAGCAGGATCAAAAATCCACTAAATCTGTTTTAGGTCTCAGACATCTTGTGCACTACAAAATACCAAA
AGCCATAAGCTAAAGTCCTAATTTGATAGTTGGAAATTTTAGTTCAGTCATTCCAAGCACCCCTAACATAATAGCAAATG
GCATTAGTGGGAATAAATCCAGTGGCAGCTATCAGCAAAAAGTTAGAATTATTTTCTCA

Alignment

ORF - retro_cfam_858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.12 %
• Parental protein coverage: 53.01 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  AAKGKLKCQTTKP-YLKAKSNRLNPPPSKSNIIPKKDVTNHVALPIKATRPISIKLQPRPGNLMGS-QKP
          A.....KCQ..KP.Y.KAKSN.LN..P..S.I.PKKDVTNH..LPIKA.R.ISIK.QPRP.N..GS.QKP
Retrocopy APRSNTKCQNAKP>YVKAKSNCLNLLPFESIIMPKKDVTNHINLPIKAIRSISIKPQPRPTNITGS<QKP

Parental  KLEPPKLLGRRLTSGCVSSNSNCKPSSKGQQ-HKAVSSTTEELSR-KTMGSLNMQELKTAKQQVADQGNT
          KLE.PKL.G.R.T.G..SSN.N..PSS..QQ.H...SSTTEE.SR.K..G.......KTAK.QVADQGN.
Retrocopy KLETPKLPGKRQT*G*ISSNLNRQPSSNSQQQHETGSSTTEEVSR<KNCGVT*YIAPKTAKKQVADQGNV

Parental  KYADSVNSNHIENEPLDSF-LKEMNKENLPQTLP-DSETKPNPELWAIGKPKTNSYNQVKSSLAPKQALG
          K.ADSV..NH.ENE.L..F.LKE.N...L....P...E.KPNPEL..IGKPK..SYNQ.KSSLAPK.ALG
Retrocopy KCADSVDNNHVENESLNTF<LKEINTKRLA*NFP<QTERKPNPELQTIGKPKIISYNQTKSSLAPK*ALG

Parental  KGSGNSAVLKDRVNKQFVGKTQIRTPPVKSQQLSRGTNLARPGEKLPKTVPSHNVQTLGRTQASKKTVVK
          K.SGNSA.LKDRVNK.FV...QIR.PP.K.QQL.RGTNLAR.GEK..KTV.SH.VQ.L.RT..SKK.V.K
Retrocopy KISGNSAILKDRVNKEFVREPQIRIPPQKPQQLLRGTNLARTGEKFSKTVLSHYVQPLSRTLKSKKPVIK

Parental  DIKDIKVNRDNSERPNESKVQSHTVTEQKVKQTKPWTCPSVLRGGFNNRHPNIKQDQKSTQP-CSKTQTS
          DIK...VN.D...RPNE.K.QSHT.TEQ..KQ.KPWTCPSV..GG..NRH.N.KQDQKST...C...QTS
Retrocopy DIK---VNGDKYKRPNEIKLQSHTATEQNIKQSKPWTCPSVFQGGYSNRHSNKKQDQKSTKS<CFRSQTS

Parental  CAPQKS-KRTSQRPNLAVGSFNSVIPSTPVITANGTSGNKCRNSYEQKAQTLDS
          CA.Q...K..S..PNL.VG.F.SVIPSTP.I.ANG.SGNK...SY.QK.....S
Retrocopy CALQNT>KAIS*SPNLIVGNFSSVIPSTPNIIANGISGNKSSGSYQQKVRIIFS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	4.16 RPM
SRP017611_brain	0.00 RPM	0.32 RPM
SRP017611_kidney	0.00 RPM	0.40 RPM
SRP017611_liver	0.00 RPM	0.29 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_858 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_858 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_858 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968,
Canis familiaris	ENSCAFG00000007242	1 retrocopy	retro_cfam_858 ,
Cavia porcellus	ENSCPOG00000010435	2 retrocopies	retro_cpor_229, retro_cpor_528,
Felis catus	ENSFCAG00000028904	1 retrocopy	retro_fcat_615,
Mustela putorius furo	ENSMPUG00000009729	1 retrocopy	retro_mputfur_1172,
Ochotona princeps	ENSOPRG00000012796	1 retrocopy	retro_opri_904,
Tupaia belangeri	ENSTBEG00000013625	2 retrocopies	retro_tbel_1637, retro_tbel_4436,