RetrogeneDB ID: retro_cfam_960

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 20:31992315..31993653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1C
• Ensembl ID: ENSCAFG00000008661
• Aliases: None
• Description: tubulin, alpha 1c [Source:HGNC Symbol;Acc:20768]

Sequence

>retro_cfam_960
GAGTGTATCTCCATCCACATTAGACAGGTTGGTGTCTAGATCAGCAATGCCTGCTGGGAGCTCTGTTGCCTAGAACATGG
CATTCAGCCCAATGGCCAGATGCCAAGTGACAAAACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCAGTGAGA
CAGGGGCTGGCAAGCATGTGCCCAGGGAAGGGTTTGTAGACCTGGAACCCACGGTCATTGATGAAGTTTGCACTGGCACC
TACTCAGGCTCTTCCACCCTGAGTAGCTCATCACAAGCAAGGAAGATACTGCCAATAACTATGCCCAAGGGCATTACACC
ATTGACAAGATCATTGATCTTGTCTTGGGCCAAATTAGGAAGCTTGGTTGACCAGCACTTGGTTCTTCAAGGCTTTTTGG
TTTTCCACAGCTTTTGGAGTGGGAACTGGTCCCAGGCTTAACACCCTGCTGATGGAACATCTCTCTGTCAAACATGGCAA
GAAGTCCAAGCTGGAGTTCTCCATTTAGCCAGGCCCCCAGATTTCTATAGCTGGATTCGAGCCCTACAACTCCATCCTCA
CTACCCACACACCCTGGAGCACTCTGACTGTGCCTTCACAATAGACAACAAGGCTATCCATGACATCTGTCATAGAAACG
TCACTATTGAACACCCAACCTGCACCAACCTTAACTACCTTATTAGCCAGACTGTGTTTTCCATCACTGCTTCCCTCAGA
TTTGACGGAGCCCTGAATATTGCTCTGATGGAATTCCACATGAAACTGGTGCCCTATCCCTGCATCCACTTTCCTCTGGC
CACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTACTGTAGCAGAGATCACCAATGCGTGCTTTG
AACCAGCCAACCAGATGGTGAAGTGTGACCCTTGTCATGGTAAATATATGGCCTGCTGCCTGTTGTACCATGGCAACATG
GTTCCCAAAGATGTCGATGCTGCCATTGTCACCATCAAGACCAAGTGTACCATCCAGTTTGTGGACTGGTGTCCCACTGG
CTTAAAAGTGGGCATTAATTGCCAGTCTTCCACTGTGGTACCTGGTGAAGACCTGGCCAAAGTACAGAGAGTTGTGTGCA
TGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGATTGCCTGGACCACAAGTTTGACCTAATGTGTGCCGAGCATGCC
TTTGTTCACTAGTATGTGGATAACAGCATGGAGGAAGGAGAGTTTTCTGAGGCCTGTGAGGACACAGCTGCCTTAGAGAA
GGATTATGAAGAGTTTGGATCAGATAGTGCTGAGGGAGAGGATGAGGGTAAAGAGTAT

Alignment

ORF - retro_cfam_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.04 %
• Parental protein coverage: 87.48 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEP
          ECISIH..Q.GV.I.NACWEL.CLEHGIQP.GQMPSDKTIGGGDDSFNTFFSETGAGKHVPR..FVDLEP
Retrocopy ECISIHIRQVGV*ISNACWELCCLEHGIQPNGQMPSDKTIGGGDDSFNTFFSETGAGKHVPREGFVDLEP

Parental  TVIDEVRTGTYR-QLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLA-DQCTGLQGFLVFHS
          TVIDEV.TGTY...LFHPE.LIT.KED.ANNYA.GHYTI.K.IIDLVL..IRKL..DQ...LQGFLVFHS
Retrocopy TVIDEVCTGTYS<RLFHPE*LITSKEDTANNYAQGHYTIDK-IIDLVLGQIRKLG>DQHLVLQGFLVFHS

Parental  F-GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHT-TLEHSDCAFMVDNEA
          F.G.GTG.....LLME.LSV..GKKSKLEFSI.P.PQ.S.A..EPYNSILTTHT.TLEHSDCAF..DN.A
Retrocopy F>GVGTGPRLNTLLMEHLSVKHGKKSKLEFSI*PGPQISIAGFEPYNSILTTHT<TLEHSDCAFTIDNKA

Parental  IYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISA
          I.DIC.RN..IE.PT.TNLN.LISQ.V.SITASLRFDGALN..L.EF...LVPYP.IHFPLATYAPVISA
Retrocopy IHDICHRNVTIEHPTCTNLNYLISQTVFSITASLRFDGALNIALMEFHMKLVPYPCIHFPLATYAPVISA

Parental  EKAYHEQLTVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCP
          EKAYHEQLTVAEITNACFEPANQMVKCDP.HGKYMACCLLY.G..VPKDV.AAI.TIKTK..IQFVDWCP
Retrocopy EKAYHEQLTVAEITNACFEPANQMVKCDPCHGKYMACCLLYHGNMVPKDVDAAIVTIKTKCTIQFVDWCP

Parental  TGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEF
          TG.KVGIN.Q..TVVPG.DLAKVQR.VCMLSNTTAIAEAW..LDHKFDLM.A..AFVH.YV...MEEGEF
Retrocopy TGLKVGINCQSSTVVPGEDLAKVQRVVCMLSNTTAIAEAWDCLDHKFDLMCAEHAFVH*YVDNSMEEGEF

Parental  SEAREDMAALEKDYEEVGADSAEGEDEGEEY
          SEA.ED.AALEKDYEE.G.DSAEGEDEG.EY
Retrocopy SEACEDTAALEKDYEEFGSDSAEGEDEGKEY

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	45.95 RPM
SRP017611_brain	0.00 RPM	6.27 RPM
SRP017611_kidney	0.00 RPM	120.19 RPM
SRP017611_liver	0.00 RPM	19.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_960 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
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,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Erinaceus europaeus	ENSEEUG00000004068	1 retrocopy	retro_eeur_669,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,