RetrogeneDB ID: retro_btau_1726

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:2111578..2112205(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGC143285
• Ensembl ID: ENSBTAG00000001999
• Aliases: None
• Description: None

Sequence

>retro_btau_1726
ATTAGAGAACTGGAGAAACAGATGGAAGATGCTTACTGGGGGACCAAAAGGAAAATATGACCCAGTAGTTCAAGCCAGAT
ACCTAATGATGGTTTTGATGAAGCAAGTCAAGAGACTATTGGAAGTCAAAGAATGAAATTTATGGAGCAGTGGATGATGA
TTTTCTTAAGGCTAAATCCTGGAACAAGTAGTTATATGATTATGAAGCTAACACACCAGACAGATGGGGTCACAGTGGCT
ATAAAGAGTTATACCCTCAGGAATCTGAAACAGACAGTGATCAACAAGATAGTACATGCTATCTAATGGGGAAAAAACAT
CTCCCCAGGTAAAATCATCTACCCACAAACATAAAAAGTCAAAGAAATCCCACAAAGAAATAAGAAAAAAAAAATCACAC
AAAAACCAGAAGAAAAGCAAAAAGGAAACCACAGATAGAACAGCTGATTCCTCAAGTGAGATCTCAGAAGAAACTGGGGC
TTCTATTGCTAGGAAAAGGAGACAACCACAGAAGCTGAAGAAAAAATCCAGGAAAAGTCTCTCAAGAAATCTGCTTTATT
CCTAGAGGCAGAAAGTGACACATCCCAGTCAGATGATTCTGCATCCAGCAGTTCAGTGGGAAGTGAG

Alignment

ORF - retro_btau_1726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.89 %
• Parental protein coverage: 79.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IRELEKQMDDAYRGTKRRMLPSSSSRMRSDGFDEESQ-RDYWRPKNEICGALDDGFLKAKSWNKKLYDYE
          IRELEKQM.DAY.GTKR...PSSSS....DGFDE.SQ.RDYW..KNEI.GA.DD.FLKAKSWNK.LYDYE
Retrocopy IRELEKQMEDAYWGTKRKI*PSSSSQIPNDGFDEASQ<RDYWKSKNEIYGAVDDDFLKAKSWNK*LYDYE

Parental  ANMPDRWGHSGYKELYPEEFETDSSDQQDIT---NGKK-TSPQVKSSTHESHKHKKSKKSHKKKQKKKSH
          AN.PDRWGHSGYKELYP.E.ETD.SDQQD.T....GKK.TSPQVKSSTH...KHKKSKKSHK........
Retrocopy ANTPDRWGHSGYKELYPQESETD-SDQQDSTCYLMGKK<TSPQVKSSTH---KHKKSKKSHKEIXXXXXX

Parental  KKQKKSKKEATDITADSSSEFSEETGASSTRKRKQPHKRKKKSRK-KSLKKSPL-LEAESDTSPSDDSAS
          ..........TD.TADSSSE.SEETGAS..RKR.QP.K.KKKSRK.KSLKKS.L.LEAESDTS.SDDSAS
Retrocopy XXXXXXXXXXTDRTADSSSEISEETGASIARKRRQPQKLKKKSRK<KSLKKSALFLEAESDTSQSDDSAS

Parental  SSSEESE
          SSS..SE
Retrocopy SSSVGSE

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	5.84 RPM
ERP005899_muscle	0.05 RPM	6.97 RPM
SRP017611_brain	0.00 RPM	6.12 RPM
SRP017611_kidney	0.00 RPM	11.08 RPM
SRP017611_liver	0.00 RPM	5.81 RPM
SRP030211_testis	0.01 RPM	25.04 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1726 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1726 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001999	1 retrocopy	retro_btau_1726 ,
Cavia porcellus	ENSCPOG00000011060	1 retrocopy	retro_cpor_1008,
Monodelphis domestica	ENSMODG00000014393	1 retrocopy	retro_mdom_351,
Tursiops truncatus	ENSTTRG00000010518	1 retrocopy	retro_ttru_73,