RetrogeneDB ID: retro_cfam_1124

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:33895684..33896849(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBAL3
• Ensembl ID: ENSCAFG00000005248
• Aliases: None
• Description: tubulin, alpha-like 3 [Source:HGNC Symbol;Acc:23534]

Sequence

>retro_cfam_1124
GATGACTCCTTCAACATCTTCAGTGAGACAGATGCTGGCAAGCATGTACCCAGGGCAGTGTCTGTAGACCTGAAACCCAG
AGTCATTGATGAAGTTCACAATGGCACCTACCACCAGCTTTTCCACCCTCAGCAGCTCATCGCAGGCAAGAAAGATGCTG
CCAAGAACTATGCCTAAGGACACTATACCATTGACAAAGAGATCATTGACCTTGTCTTGGAATGAATTTGTTAAGTGGCC
AGTGAGTACACAGGTCTTCAGGGCTTCTTGGTTTTCCACAGTTTTGGAGGGGGAACTGGTTCCAGGTTCACCTCTCTGCT
GATGGAACATCTTTGTCAGTTATGGCAAGAAGTCCAAGTTGGAGTTCTTCATTTACTCTGTCCCCCAGATTTCCACAGCT
GTAGCTAAGCCCTACAGCTCCATCCTCACCACCCACAGCACCCTGGAACACTGAGATTGTGCCTTAATGACAGACAATGA
GGCCATCTATGACATATATCATAGAAACCTTGATATTGAATGCCCAACCTACACTAACCTAAGTAGGTTGATAGGTTAAA
TTGTGTCCTCCATCACTACTTCCCTAAGATTTGATGGAGCCCTGAATGTTGATCTAACAGACCTCCAGACCAACCTAGTG
CTCTATCCCCACTTCTAGTTTCCTCTGGTCATATATATTCCTGTCATTTCTGCTGAGAAAGCCTACCATGAACAGCTTTC
TGTAGGAGAAATCACTGATGCATGCTTTGAGCCAGTCAACCAAATGGTGAAATGTGCCCCTTGCCATGGTAAATACATGG
CTTGCTGCCTGTGGCACCATAGTGACATGGTCCTAAAGATGTCAGCACTGCCATTGCCGCCATCAGGACCAAACATACCA
TCCACTTTGTAGACTGGTGCTCCACTGTGCTTCAAAGTTGGCATTAATTACTAGCCTCCGACTGTGGTACCTGGTAGAGA
CCTGGCCAAAGTATGCAAGCTGTGTGTATACTGAGCAACAGCACAGCCATTGCTGAGGCATAGGCTAACCTGGACCATAA
GTTTGACCTGATATATGCCAAGCATGCCTTTGTTCAGTGGTATGTAAGAAGGGCATGAATGAAGAGAGTTTTCTGAGGCC
CATGAGGACATGGCTGCCCTTGAGAAGGATTATAAGGAGGTTGGA

Alignment

ORF - retro_cfam_1124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.55 %
• Parental protein coverage: 98.24 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  DASFNTFFCETSTGKHVPRALFMDLEPTVIDGIRAGPRRALFHPEQLVSGKEDAANNYARGRYSVGSGII
          D.SFN..F.ET..GKHVPRA...DL.P.VID....G....LFHP.QL..GK.DAA.NYA.G.Y.....II
Retrocopy DDSFN-IFSETDAGKHVPRAVSVDLKPRVIDEVHNGTYHQLFHPQQLIAGKKDAAKNYA*GHYTIDKEII

Parental  DLVLERIRKLTEQCSGLQGFLVFRSCGGGTGSGFTSLLMEKLSMEY-SRKTKLEFSVYPAPR-ISTAIVE
          DLVLE.I........GLQGFLVF.S.GGGTGS.FTSLLME.L......R......S....PR.ISTA...
Retrocopy DLVLE*IC*VASEYTGLQGFLVFHSFGGGTGSRFTSLLMEHLCQLW<ARSPSWSSSFTLSPR<ISTAVAK

Parental  PYNSILTTHSTIEHSDCTFLVDNEAIYDICHHKLGVECPSYASINRLIGQAVSSITTSLRFEGPLNVDLI
          PY.SILTTHST.EH.DC....DNEAIYDI.H..L..ECP.Y....RLIG..VSSITTSLRF.G.LNVDL.
Retrocopy PYSSILTTHSTLEH*DCALMTDNEAIYDIYHRNLDIECPTYTNLSRLIG*IVSSITTSLRFDGALNVDLT

Parental  EFQTNLVPYPRIHFPTTTFAPIISAESAYREELSVCDITAACFDFSNQLVKCNPRLGKYMACCLLYRGDV
          ..QTNLV.YP...FP.....P.ISAE.AY.E.LSV..IT.ACF...NQ.VKC.P..GKYMACCL....D.
Retrocopy DLQTNLVLYPHF*FPLVIYIPVISAEKAYHEQLSVGEITDACFEPVNQMVKCAPCHGKYMACCLWHHSDM

Parental  V-PKDVNSAIAAMKSRNSVQFVDWC-PTGFKVGINSQPPTVMPGGDLAKV-QRAVCMLSNNTAVVEAWAR
          V.PKDV..AIAA........FVDWC.P..FKVGIN..PPTV.PG.DLAKV...AVC.LSN.TA..EA.A.
Retrocopy V<PKDVSTAIAAIRTKHTIHFVDWC>PLCFKVGINY*PPTVVPGRDLAKV<MQAVCILSNSTAIAEA*AN

Parental  LDHKFDLMYAKRAFLHWYTR-EGMEED-EFSEAREDLAALEKDYEEMG
          LDHKFDL.YAK.AF..WY.R..GM.E..EFSEA.ED.AALEKDY.E.G
Retrocopy LDHKFDLIYAKHAFVQWYVR<KGMNEE<EFSEAHEDMAALEKDYKEVG

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	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.79 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1124 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1124 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005248	1 retrocopy	retro_cfam_1124 ,
Canis familiaris	ENSCAFG00000008640	8 retrocopies	retro_cfam_1481, retro_cfam_1751, retro_cfam_1895, retro_cfam_1917, retro_cfam_1979, retro_cfam_2000, retro_cfam_463, retro_cfam_926,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Canis familiaris	ENSCAFG00000010412	1 retrocopy	retro_cfam_1418,
Equus caballus	ENSECAG00000014631	1 retrocopy	retro_ecab_147,