RetrogeneDB ID: retro_btau_402

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:46014780..46015810(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSBTAG00000012244
• Aliases: None
• Description: Tubulin alpha-1B chain [Source:UniProtKB/Swiss-Prot;Acc:P81947]

Sequence

>retro_btau_402
ATCTCCTTCCACGTTGGCCAGGCTGGTGTCCACATAGGCAATGCCTGCTGGGAGCTCTACTGCCTAGAACACAGCATCCA
GCCTGATGGCCAGATGCCAAGTGACAAGACTACTGGGGGAGAAGATGACACCTTCAACACCTTCTTCAGTGAGACAGGTG
CTGGCAAGCGTGTGCCCAGGGCAGTGTCTGCAGACCTGGAACCCACAGTTATTGATGAGGTTCGCACTGGCACCTACTTC
CAGCTCCTCCACCCTGAGCAGCTTATCACAGATAAAGAAGATGCTGCCAGTAACTGTGCCTGAGGTCACTATACCATTGG
CAAGGAGATCATTGATCTTGTCTTGGACCGAATTTGGAAATTGGCTGACCAGTGCACAGGTCTCCAGGGCTTCTTGGTTT
TCACAGCTTTGGTGGGGGAACTGGTTCTGAGTTTGCCTCCCTGCTGATGGAACATCTCTCTGTTGATTATAGCAAAAAGT
CCAAGCTGGAATTATTTATTTACCCAGCCCTCCAGGTTTCCACAACTGTAGTTTAGCCCTACAACACCATCCTCACCACC
ACACCATCCTGGAGCATCTGATTTTGCCTTCATGATAGACAATGAGGCCATCTATGACACCTGCTGTAGAAACCTTGATA
TTGAGCACCCAACCTACATGAATCTTAACTGCCTATTAGCCAGATAGTGTCCCCAATCACTGCTTCCCTGAGGTCTGATG
GAGCCCTGACTGTGGATCTGACAGAGTTCCAGACCAACCTGGTGCTCTATCCCCACATTCACTTCCCTCTGGCCACATAC
ACCCCTGTCATCTCTGCAGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATGCTTGCTTTGAGCCATC
CAACCAGATGGAGAAATGTGACCCTCGTGATGGTAAATACATGGCCTGCTGCCTGTTGTACTATGGTGACGTGGTTCCCA
AAGATGTTGTACCACCATTATCACCATCAAGACCAAGTGCATCATCCAGTTCGTGGCCTGGTGCCCCACT

Alignment

ORF - retro_btau_402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 76.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTV
          IS.HVGQAGV.IGNACWELYCLEH.IQPDGQMPSDKT.GG.DD.FNTFFSETGAGK.VPRAV..DLEPTV
Retrocopy ISFHVGQAGVHIGNACWELYCLEHSIQPDGQMPSDKTTGGEDDTFNTFFSETGAGKRVPRAVSADLEPTV

Parental  IDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLV-FHSFGG
          IDEVRTGTY.QL.HPEQLIT.KEDAA.N.A.GHYTIGKEIIDLVLDRI.KLADQCTGLQGFLV.FHSFGG
Retrocopy IDEVRTGTYFQLLHPEQLITDKEDAASNCA*GHYTIGKEIIDLVLDRIWKLADQCTGLQGFLV<FHSFGG

Parental  GTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTT-HTTLEH-SDCAFMVDNEAIYD
          GTGS.F.SLLME.LSVDY.KKSKLE..IYPA.QVST.VV.PYN.ILTT.HT.LEH.SD.AFM.DNEAIYD
Retrocopy GTGSEFASLLMEHLSVDYSKKSKLELFIYPALQVSTTVV*PYNTILTT<HTILEH<SDFAFMIDNEAIYD

Parental  ICRRNLDIERPTYTNLNRL-ISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          .C.RNLDIE.PTY.NLN.L.ISQIVS.ITASLR.DGAL.VDLTEFQTNLV.YP.IHFPLATY.PVISAEK
Retrocopy TCCRNLDIEHPTYMNLNCL<ISQIVSPITASLRSDGALTVDLTEFQTNLVLYPHIHFPLATYTPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDV-NAAIATIKTKRSIQFVDWCPT
          AYHEQLSVAEITNACFEP.NQM.KCDPR.GKYMACCLLY.GDVVPKDV....I.TIKTK..IQFV.WCPT
Retrocopy AYHEQLSVAEITNACFEPSNQMEKCDPRDGKYMACCLLYYGDVVPKDV<CTTIITIKTKCIIQFVAWCPT

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	35.33 RPM
ERP005899_muscle	0.00 RPM	480.75 RPM
SRP017611_brain	0.00 RPM	593.79 RPM
SRP017611_kidney	0.12 RPM	112.56 RPM
SRP017611_liver	0.00 RPM	69.47 RPM
SRP030211_testis	0.00 RPM	49.61 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_402 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_402 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 31 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,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,