RetrogeneDB ID: retro_btau_350

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:69776342..69777686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.53243
• Ensembl ID: ENSBTAG00000001489
• Aliases: None
• Description: tubulin alpha-1B chain [Source:RefSeq peptide;Acc:NP_001159977]

Sequence

>retro_btau_350
ATGTGTGAGTGCATCTCCATCCACTTTGGCCAGGTTGGTGTTCAGACAGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACATGGCCTTCAGCCCGATGGCCAGATGCCAAGTGACAAGACTACTGGGGGAGGAGATGACTCCTTCGACACCTTCTTCA
GTGAGACAGACACTGGCAAGCATGTGCCCAGGGCAGTGTTTGTAGACCTGGAATCCCCACTCATTGATGAGGTGTGCACT
GGCACCTACTGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAAGAGGATGCTGCCAGTAATTGTGCCCGAGGTCA
CCACACCACTGGCGAGGAGATCACTGACCTCATCTTGGACCAGATTCAGAAACTGGCTGAGCAGTGCACAGGTCTTCAGG
GCTTCTTGGTTTTTCACAGCTTTGGTGGGGGAACTGGTTCTGGGTCACCTCATTGCTGATGGAATGTCTCTGTCGATTAT
GGCAAGAAGTCCAAGCTGGGGTTCTCCATTTACCCAGCCCCACAACTTTGAACAGCTGTAGCTGAGCCCTACAACTCCAT
CCTCACCACCCACACCACCCTGAAGCACTCTGATTGTGCCTTCGTGGTAGACAATGAGGCCATCAATGACATCTGTCCTA
GAAAACTCGACATTGAGTGCCCAGCATATATTAACCTGAATAGGTTGATAGGTCAAATTGTGTCCTCCGTCACTGCTTCC
CTGAGGTGTGAAGGAGCCCTGAATGTGGATCCAACAGAGTTCCAGACCAACCTGGTGCCCTATCCCCGCATCCACTTCCC
TCTGGCCACATACGCCCCTGTCATCTCTGCTGAGAAAGCCCACCGTGAATAGCTTTCTGTAGCAGAGATCACCAATGCTT
GCTTTGAACCAGCCAACCGGAAGGTGAAATGTGACCCTTGCCGTGGTAAATACATGGCCTGCTGCCTGTTGTACCGTGGC
GACATGGTTCCCAAAGATGTCAGTGCTGCCAGTGCCACCATCAAAACCAAGCGTACCATCCAGTTTGTGGACTGGTGCCC
CAGTGGCTTCAAGGTTGGCATTAATTACCAGCCTCCTGCTGTGGTCCCTGGTGGAGACCTGGCCAAAGTAAAGCAAGCTG
TGTGCACGCTGAGCAACACCACAACCACCACTGAGGCCTGGACTCACCTAGACCACAATCTGATGTATACCAAGCATGCC
TTTGTTCACTGGTACATGGGTGAGGGCATGGAGGAAGGAGAGCTTTCTGAGGCCCATGAGGCCATGGCTTCCCTTGAGAA
GGATTATGAGGATGTTGGTGTAGATTCTGTGGAAGGAGAGGGAGAGGAAGAAGGAGAGGAATAC

Alignment

ORF - retro_btau_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          M.ECISIH.GQ.GVQ.GNACWELYCLEHG.QPDGQMPSDKT.GGGDDSF.TFFSET..GKHVPRAVFVDL
Retrocopy MCECISIHFGQVGVQTGNACWELYCLEHGLQPDGQMPSDKTTGGGDDSFDTFFSETDTGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          E...IDEV.TGTY.QLFHPEQLITGKEDAA.N.ARGH.T.G.EI.DL.LD.I.KLA.QCTGLQGFLVFHS
Retrocopy ESPLIDEVCTGTYCQLFHPEQLITGKEDAASNCARGHHTTGEEITDLILDQIQKLAEQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          F.GG.............SVDYGKKSKL.FSIYPAPQ..TAV.EPYNSILTTHTTL.HSDCAF.VDNEAI.
Retrocopy F-GGGTGSGSPHC*WNVSVDYGKKSKLGFSIYPAPQL*TAVAEPYNSILTTHTTLKHSDCAFVVDNEAIN

Parental  DICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DIC.R.LDIE.P.Y.NLNRLIGQIVSS.TASLR..GALNVD.TEFQTNLVPYPRIHFPLATYAPVISAEK
Retrocopy DICPRKLDIECPAYINLNRLIGQIVSSVTASLRCEGALNVDPTEFQTNLVPYPRIHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTG
          A..E.LSVAEITNACFEPAN..VKCDP..GKYMACCLLYRGD.VPKDV.AA.ATIKTKRTIQFVDWCP.G
Retrocopy AHRE*LSVAEITNACFEPANRKVKCDPCRGKYMACCLLYRGDMVPKDVSAASATIKTKRTIQFVDWCPSG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          FKVGINYQPP.VVPGGDLAKV..AVC.LSNTT...EAW..LDH...LMY.K.AFVHWY.GEGMEEGE.SE
Retrocopy FKVGINYQPPAVVPGGDLAKVKQAVCTLSNTTTTTEAWTHLDH--NLMYTKHAFVHWYMGEGMEEGELSE

Parental  AREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          A.E.MA.LEKDYE.VGVDSVEGEGEEEGEEY
Retrocopy AHEAMASLEKDYEDVGVDSVEGEGEEEGEEY

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
ERP005899_liver	0.00 RPM	3.53 RPM
ERP005899_muscle	0.00 RPM	20.96 RPM
SRP017611_brain	0.00 RPM	359.36 RPM
SRP017611_kidney	0.00 RPM	19.68 RPM
SRP017611_liver	0.00 RPM	4.68 RPM
SRP030211_testis	0.01 RPM	77.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_350 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350 , retro_btau_929,
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840,
Callithrix jacchus	ENSCJAG00000020894	2 retrocopies	retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus	ENSDNOG00000004121	1 retrocopy	retro_dnov_43,
Equus caballus	ENSECAG00000013798	1 retrocopy	retro_ecab_223,
Homo sapiens	ENSG00000167552	1 retrocopy	retro_hsap_3313,
Nomascus leucogenys	ENSNLEG00000017836	2 retrocopies	retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus	ENSOCUG00000027812	1 retrocopy	retro_ocun_197,
Pteropus vampyrus	ENSPVAG00000004645	2 retrocopies	retro_pvam_1283, retro_pvam_414,
Rattus norvegicus	ENSRNOG00000004559	3 retrocopies	retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos	ENSVPAG00000005749	4 retrocopies	retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72,