RetrogeneDB ID: retro_cfam_968

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:46428218..46429754(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2
• Ensembl ID: ENSCAFG00000005898
• Aliases: None
• Description: cytoskeleton associated protein 2 [Source:HGNC Symbol;Acc:1990]

Sequence

>retro_cfam_968
CCGAAGCGAGATGCTAACATGTCCAAGAAGCTTGTGCTTCGGTCTTACCGTGTTCAAACTGTTCAGTCTAAGATTAATTC
ATTTAGAAAGCCCCTACCAGTCAGAGATGAGAGTTCTGCAGCAACAAAGAAACTTTCAGCAACTATCCTAAAGCCCCAGA
GCCTCTGCCTGCAGACACTTGCAGTTTGACAGTGAGAAGTGACACAACCCGAAACATGATGACCACCACTAGACTTGTGA
GCACTGCCTCTCAAGACAGACAGCTGGTGTGGCCTCCTATCAGAAGTCACGACAATAGTGCTTTGGGACCTTGTGAAACA
AGGCATCAGGAGAACTGCTGCCAATGTTACAATCCAGAAAGGGCCTCAGGAGAAGGAATTACTGCAATCAAACACAGTTT
CATCTAGAGCCAAAACCAGTTCTCAGGATGTAGAGAGAAAGAAGACACTGTCAAGAAACCTGACGTCTGAAATTGTAGCC
AGGCCTGCTTCATCTTCTAACTCCAGACTGATTCAGAAGTCAAAAAGCATTGACTCTCACAGACACACTATAGCAAAAGC
AACTATTGATAGATCAACTCAGCCCAAAGAAACAGCAAAAGAAAGAAAAGCTTGTCTGAGTGAGTGGAAAGCTAGCAAAA
GAAAAGTGCTGAAAAGCCCTCCTAGCTCAGGAGTTACCCAGCCTGAAGGGCGAAATGAAAACTCAGTTGGGTCCTTTTGG
ACTACCATGGTAGAAGAATATGAACAAAGATTATTTACTGAAAATGTGAACAAGACATTTTCTGAATGCCTAAACCTGAT
TAATAAGGGGTGCCCAAAAGAAGAAATATTAGTCATACTGAATGACCTGATTAAAAATATTCCAGATGCCAAAAAACTTG
TTAAGTATTGTGTATGCCTTGCACGTATTGAACCACTTCACAAGCTCTATTCAACATATCACAATCTATGAGAAAGCTAT
TTTGGCAGGGGCTCAGCCTATCGAAGAAATGCGACACGTAATTGCAGATATTATAACAATGAAGAGTCCAGAAAAAGTCA
AATATGGAGAAAATGTTGAGGCTTGTGCAACCAAGGAATACATCCAGGATATCAGCAGTGAAGATATAGGTGTTAATCTA
GAGTCAGGAAAACCAGAAATGGAAAAGAAACCTAGAAACGTGGTATTTCAAGATGACAAACAAGAGCAAGATGACAAAAC
AAAAGATCTAACCAATGATGTTAAAACTGTGCAGAAACTGGGGGGAGCTGCTTAATTAAATATAATGTGTCTACTACACG
ATACCTACAAAGTATGAAAAAGAAGATACAGTTTGACAATACAGATTCTACATTTAAAGAGTTAAAGTTTCTAACACCAG
TTAGACGTTCTCAACCTATTCAAGAGAAGATTTCTTAATTGCCAGATATGTTAAAAGACCATTATCCACCCATCTCTTCA
CTGGAGCAGTTAACAGAGTTGGGAGGTGAAACTGATGCTTTTGTATGGCATCCTAACACAGCCCTATGCCTGATGTACTC
AGAGACTGGAACAGCA

Alignment

ORF - retro_cfam_968 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.6 %
• Parental protein coverage: 76.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PKQDANMPKKLVLGSYNGQIVQSKINSFRKPLPVRDESSVATKKLSATI-PKAPEPLPADTSSFTVRSHR
          PK.DANM.KKLVL.SY..Q.VQSKINSFRKPLPVRDESS.ATKKLSATI.PKAPEPLPADT.S.TVRS..
Retrocopy PKRDANMSKKLVLRSYRVQTVQSKINSFRKPLPVRDESSAATKKLSATI<PKAPEPLPADTCSLTVRSDT

Parental  APNVMTTTRPVSTASQDRRLVRPPIRSHCNSAQDP-VKQGIRRS---LTIRKGPQEKELLQLNTVSSSAK
          ..N.MTTTR.VSTASQDR.LV.PPIRSH.NSA..P.VKQGIRR.....TI.KGPQEKELLQ.NTVSS.AK
Retrocopy TRNMMTTTRLVSTASQDRQLVWPPIRSHDNSALGP>VKQGIRRTAANVTIQKGPQEKELLQSNTVSSRAK

Parental  TSSQDVERKTTVSRSLMSKIVARPASSFNTRLIQKSKSIDPCRHSVAKATIDRSIHPKETAEERKARLSE
          TSSQDVERK.T.SR.L.S.IVARPASS.N.RLIQKSKSID..RH..AKATIDRS..PKETA.ERKA.LSE
Retrocopy TSSQDVERKKTLSRNLTSEIVARPASSSNSRLIQKSKSIDSHRHTIAKATIDRSTQPKETAKERKACLSE

Parental  WKASKRKMIKRPPSSGVTQSEPEGRNEKSSGSFWTTMVEEDEQRLFTEKVNKTFSECLNLINEGCPKEEI
          WKASKRK..K.PPSSGVTQ..PEGRNE.S.GSFWTTMVEE.EQRLFTE.VNKTFSECLNLIN.GCPKEEI
Retrocopy WKASKRKVLKSPPSSGVTQ--PEGRNENSVGSFWTTMVEEYEQRLFTENVNKTFSECLNLINKGCPKEEI

Parental  LVILNDLIKDIPDAKKLVKYWICLARIEPL-TSPIENIITIYEKAILAGAQKIKPIEEMRHVIADILTMK
          LVILNDLIK.IPDAKKLVKY..CLARIEPL.TS.I...ITIYEKAILAGAQ...PIEEMRHVIADI.TMK
Retrocopy LVILNDLIKNIPDAKKLVKYCVCLARIEPL>TSSIQH-ITIYEKAILAGAQ---PIEEMRHVIADIITMK

Parental  SQEKVKYGENVEACATKEYIQDVSSEDIGVNLESGKPETEKKPRNVVFQDDEKKQDDKTKYLTNDVKTPS
          S.EKVKYGENVEACATKEYIQD.SSEDIGVNLESGKPE.EKKPRNVVFQDD...QDDKTK.LTNDVKT..
Retrocopy SPEKVKYGENVEACATKEYIQDISSEDIGVNLESGKPEMEKKPRNVVFQDDKQEQDDKTKDLTNDVKTVQ

Parental  AETGG-SCLIKYNVSTTPYLQSIKKKIQFDNTDSTFKELKFLTPVRRSQRIQEKTSKLPDMLKDHYPCVS
          ...GG.SCLIKYNVSTT.YLQS.KKKIQFDNTDSTFKELKFLTPVRRSQ.IQEK.S.LPDMLKDHYP..S
Retrocopy -KLGG<SCLIKYNVSTTRYLQSMKKKIQFDNTDSTFKELKFLTPVRRSQPIQEKIS*LPDMLKDHYPPIS

Parental  SLEQLTELGGETDVFVCRPNTALCPMYSETGTA
          SLEQLTELGGETD.FV..PNTALC.MYSETGTA
Retrocopy SLEQLTELGGETDAFVWHPNTALCLMYSETGTA

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	0.08 RPM	19.03 RPM
SRP017611_brain	0.08 RPM	8.97 RPM
SRP017611_kidney	0.07 RPM	3.24 RPM
SRP017611_liver	0.00 RPM	0.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_968 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_968 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_968 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005898	1 retrocopy	retro_cfam_968 ,
Canis familiaris	ENSCAFG00000007242	1 retrocopy	retro_cfam_858,
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,