RetrogeneDB ID: retro_btau_729

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:51903413..51904220(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.19472
• Ensembl ID: ENSBTAG00000023840
• Aliases: None
• Description: BRISC complex subunit Abro1 [Source:RefSeq peptide;Acc:NP_001160059]

Sequence

>retro_btau_729
ATGTTCTCTTTAGATAGAAGGTATAATTAAAGGCTATCCCTCACTATTCCCAATCTAGGCAATACTAGCCAGCAAGAGTA
TAAGGTATCTTCAGTGCCAAATACTTCTCAGAATTATGCCAAAGTTATTAAAGAACATGGTACTGACTTTTTTGACAAGG
ACAGACTAATGAAAGACATCAGGGCGATTTATCAGGTTTATAATGCGCTTCAGGAGAAAGTGCCAGCAGTGTGTGCAGCC
GTAGAAAAGAGCGAGTGAGTTGTTGAATCTTGTCAGGCAGAAGTGAATCAATTAAGAAGACAAATCACTCAGAGGAAGAA
TGAAAAGGAACAAGAAAGATGATTGCCACAGGCAACACTAAGCAGACAGATGCCATCTGAAAGTGTGGACCCCACCTTCA
GCCCTCAGATGCCCTATCCAGGGTTCACAGCAGAAGGCCCAAGTACAGCTGGAGATGCAGAGCCCTCAGACCCGCCTCCG
CCTAATTCTGATCTTCACCCAAATAATCAAGAAAGTACTCTGAGCCATTCTCACATGGAAACTAGCATCTTTATGCCTCG
ACCTCAAGCCATGGACTCCTCCAGTTATGCCTCCACCAGTGCTGGACTGAAATATCTTGAAAGTGGAGCAGACCCCCTCC
TTCCCACAGAGCAGCTGGAGACAGTGCAGAGTAATCAGACGACAGTGATTGTGAAAATTTGATTGACCCTACAGAGTCCT
CTAATAGTGAATACTCACATTCAAGGGATTCTTGACCCATTGACACATCCTGATGAGGGCTCCAGGAATGCTCAGACCTC
CCAGATT

Alignment

ORF - retro_btau_729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 64.82 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFRPNRRYNQRISLAIPNLGNTSQQEYKVSSVPNTSQSYAKVIKEHGADFFDKDGVMKDIRAIYQVYNAL
          .F...RRYN.R.SL.IPNLGNTSQQEYKVSSVPNTSQ.YAKVIKEHG.DFFDKD..MKDIRAIYQVYNAL
Retrocopy MFSLDRRYN*RLSLTIPNLGNTSQQEYKVSSVPNTSQNYAKVIKEHGTDFFDKDRLMKDIRAIYQVYNAL

Parental  QEKVQAVCADVEKSERVVESCQAEVNKLRRQITQRKNEKEQERRLQQAMVSRQMPSESVDPTFSPRMPYP
          QEKV.AVCA.VEKSE.VVESCQAEVN.LRRQITQRKNEKEQER.L.QA..SRQMPSESVDPTFSP.MPYP
Retrocopy QEKVPAVCAAVEKSE*VVESCQAEVNQLRRQITQRKNEKEQER*LPQATLSRQMPSESVDPTFSPQMPYP

Parental  GFTAEGRSTLGDTEASDPPPPYSDLHPNNQESTLSHSRMESSVFMPRPQAVGSSSYASTSAGLKYPGSGA
          GFTAEG.ST.GD.E.SDPPPP.SDLHPNNQESTLSHS.ME.S.FMPRPQA..SSSYASTSAGLKY..SGA
Retrocopy GFTAEGPSTAGDAEPSDPPPPNSDLHPNNQESTLSHSHMETSIFMPRPQAMDSSSYASTSAGLKYLESGA

Parental  D-APPSHRAAGDSAEESDDSDYENLIDPTEPPNSEYSRSRDS-RPMTHPDGGSRNTQTSQI
          D..PPSHRAAGDSAE.SDDSD.ENLIDPTE..NSEYS.SRDS..P.THPD.GSRN.QTSQI
Retrocopy D<PPPSHRAAGDSAE*SDDSDCENLIDPTESSNSEYSHSRDS>DPLTHPDEGSRNAQTSQI

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	1.51 RPM
ERP005899_muscle	0.05 RPM	7.39 RPM
SRP017611_brain	0.00 RPM	4.84 RPM
SRP017611_kidney	0.00 RPM	6.99 RPM
SRP017611_liver	0.00 RPM	3.78 RPM
SRP030211_testis	0.03 RPM	6.23 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_729 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_729 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023840	1 retrocopy	retro_btau_729 ,
Choloepus hoffmanni	ENSCHOG00000007635	3 retrocopies	retro_chof_1691, retro_chof_2426, retro_chof_2563,
Equus caballus	ENSECAG00000023340	1 retrocopy	retro_ecab_839,