RetrogeneDB ID: retro_btau_1859

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:140516305..140517280(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047688
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAD51D
• Ensembl ID: ENSBTAG00000019082
• Aliases: RAD51D, RAD51L3
• Description: DNA repair protein RAD51 homolog 4 [Source:UniProtKB/Swiss-Prot;Acc:Q2HJ51]

Sequence

>retro_btau_1859
ATGGGTGTGCTCCAGGCCAGACCATGCTTGGGCCTCATCCAGGACATGGTCCAGCTCCTGCAGAGTGGTGAGATCAAGAC
AGTGGTCAATCTGGTTTCTGCAGACCTGGAGGTAGCCCAGAAAAGTGGCTTGTCTTAAAGGTCTTGGTCACCCTGAGGTG
GGCGCTGCTGGCTCAGTTCTCAGCTTTCCCCTTCAATGGTGCTGATCTGTTCAAGGAACTGAAGACTTCCACTGCCATCC
TGTCCATTGGCATTGGAAGCCTGGACAAACTGCTTTATGCTTATCTCTATACTGGAGAAGTGACTGGAATCACAGGAGGC
CCAGGTAGCAGTAAAACCCAGGTATGTCTTTGGGTGGCTGCAAACGTGGCCCACGGCTGCAACAGAATATCCTATACATC
GATTCCAATGGCAGCCTCACAGCCTCCTGCCTCCTCTAGCTACTTCAGGCCAGAACCCTGGATCAGGAAGAGCAGGCAGG
AGCTCTCCAGAGGATCCAGGTGGTGCCTGCATTTGATATCTTCCAAATGCCAAAGGTGATATAGGACCTTCCAGGTGCTG
TGATTCAGCAGGTGAGCATTTCTTCAGGGACTCTGAAGGTGGTGTTGTGGACTCTGTCCCTGTGGTGCTCATCCCACTTA
TGGGAGGTTCACAGAGGGAATACTTGGCCTTGATGCTGTAGCTGGCCCACAAGCTGAAGACTGTGGCCCAGGACCTCAGC
ATGGCAGTGGCAGTGACCAGCCACCTGATGTCAGACAGGGACAGCAGGCAGCTCAAATCTGCCCTCAAATGCTCCTGGAG
CTTTGTACCCAGCACCCAGCTTTTCCTAGACATTGGCCAAGGCACAGGAGCCTCAGGCTGCCGGCGCCTGGCATGTCTGA
CCACATCCCCTCGTCTGCCAACAGGTTTCCAAGAAACAGTGAACACTGGGACCTGTGGGGCACCAGAGCAGAGCCCAGCA
TTACAGGGAGATCAC

Alignment

ORF - retro_btau_1859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.12 %
• Parental protein coverage: 99.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGVLRAGLCPGLTQDMVQLLQSRGIKTVVDLVCADLEEVAQKCGLS-YKALVALRRVLLAQFSAFPFNGA
          MGVL.A..C.GL.QDMVQLLQS..IKTVV.LV.ADLE.VAQK.GLS..K.LV.LR..LLAQFSAFPFNGA
Retrocopy MGVLQARPCLGLIQDMVQLLQSGEIKTVVNLVSADLE-VAQKSGLS<LKVLVTLRWALLAQFSAFPFNGA

Parental  DLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGAPGSGKTQVCLCVAAHVAHG-LQQNVLYIDSN
          DL..ELKTSTAILS.GIGSLDKLL.A.LYTGEVT.I.G.PGS.KTQVCL.VAA.VAHG.LQQN.LYIDSN
Retrocopy DLFKELKTSTAILSIGIGSLDKLLYAYLYTGEVTGITGGPGSSKTQVCLWVAANVAHG<LQQNILYIDSN

Parental  GGLTASRILQLLQARTPDEEEQAGALQRIQVVRAFDIFQMLDVLQDLRGAVSQQVSSSSGTLKVV-VVDS
          G.LTAS..L.LLQART.D.EEQAGALQRIQVV.AFDIFQM..V..DL.GAV.QQVS.SSGTLKVV.VVDS
Retrocopy GSLTASCLL*LLQARTLDQEEQAGALQRIQVVPAFDIFQMPKVI*DLPGAVIQQVSISSGTLKVV<VVDS

Parental  VAAVVAPLLGGQQREGLALMMQLARELKTLARDLSVAVLVTNHMTRDRDSGQLKPALGRSWSFVPSTRLL
          V..V..PL.GG.QRE.LALM..LA..LKT.A.DLS.AV.VT.H...DRDS.QLK.AL..SWSFVPST.L.
Retrocopy VPVVLIPLMGGSQREYLALML*LAHKLKTVAQDLSMAVAVTSHLMSDRDSRQLKSALKCSWSFVPSTQLF

Parental  LDSTQSSGSLGSWRVVCLTKSPRLPTGCQETVDLGSLGTP----AFQGDH
          LD..Q..G..G..R..CLT.SPRLPTG.QETV..G..G.P....A.QGDH
Retrocopy LDIGQGTGASGCRRLACLTTSPRLPTGFQETVNTGTCGAPEQSPALQGDH

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	8.94 RPM
ERP005899_muscle	0.00 RPM	21.91 RPM
SRP017611_brain	0.00 RPM	7.22 RPM
SRP017611_kidney	0.00 RPM	16.42 RPM
SRP017611_liver	0.00 RPM	7.32 RPM
SRP030211_testis	0.00 RPM	15.64 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1859 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1859 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019082	1 retrocopy	retro_btau_1859 ,
Otolemur garnettii	ENSOGAG00000009880	1 retrocopy	retro_ogar_887,