RetrogeneDB ID: retro_btau_1619

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:71147076..71148216(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000023078
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.24640
• Ensembl ID: ENSBTAG00000015186
• Aliases: None
• Description: Acetolactate synthase-like protein [Source:UniProtKB/Swiss-Prot;Acc:A6QQT9]

Sequence

>retro_btau_1619
TTGAGAAGCAGGTGTCAGCTCATGGAGACCACGGCGGCTGCCGCCCCAGCTTGGGGCTTCTTCTCCTCTTTCCTGCTGCT
GGCCTTCAGGACGCTAGTGGCCGCCTTGCTGGGCGCCGCTCACCGCCTGGGGCTCTTCTATCAGTTGATGCACAAGGTGG
ACACGGCAAGCATCCGGCATGGTGGGGAGAATGTGGCAGCCGTGCTGAAGGCCCACGGTGTGCGCTTCCTTTTCACGCTG
GTCGGCAGGCACATTTCGCCACTGCTGGTGGCCTGTGAGAAGCCGGACATCTGCGTGGTGGACACCCACCACGAAGTCAC
AGCTGTGTTTGCCACTGATGCTGTGGCCCGCCTGACTGGGACGATGGGCGTGGCAGCAGTGACGGCCGGCCCCGGCCTCA
CCAACGCAGTGACTGCGGTGAAGAATGCCCAGATAGCCCAGTCCCCAGTCCTGCTCCTGGGTGGGGCTGCCAACACCCTG
CTGCAGAATCGGGGTGCACTCCAGGCAGTTGATCAGATAGCCCTGTTCAGGCCACTCTGCAAGTTTTGTGCTTCTGTGCG
GAGAGTACGGGATATCATCCCCACCCTGAGGGCCGCGATGGCTGCTGCACAGTCAGGCACCCCTGGCCCGGTGATTATGG
AACTGCCTCTGGACGTGCTGTACCCCTACTTCATGGTTCAGAAGGAGATGGTGCCAGGTAAGCCGCCCAAGGTCGTCATG
AGTCCAGCGGTCCACTGGTACTTAGCAAATCCCCTGGCCAACCCCTTTGCAGGAGCTTGGGAGCTTGAGCCTGAGGGGCC
TCTGCCCCTGGACATTCCCCAGGCCTCCCCCCAGCAGGTTCAGTGATGTGTGGAGATCTAGAGTTGGGCCAAAAGGCCCC
TCATGCTAATTAGGAGCCAGGCCCTGCTGCCTCCAACATCCGCAGGCAAGCTTTGGGTTGCCGTGGAGAACCTGGGCATC
CCTTGCTTCCTGGCGGGGATGGCACGGGGACTGCTGGGCCGCAACCACCCCCTCCACTTCCAGCAGAACCGCAGGGCCGC
CCTGAAGAAGGCAGACGTGGTTGTCCTGGCAGGAGCAGTGTGTCACTTCCGCCTGTCCTATGGGTGTGTCCTCAGCTGCA
GCAGCAAAATCATTGTTGTC

Alignment

ORF - retro_btau_1619 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.26 %
• Parental protein coverage: 59.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRSRCQLMETAVAAAPAWGFFSSFLLLAFGTLVAALLGAAHRLGLFYQLMHKVDTASTRHGGENVAAVLK
          LRSRCQLMET..AAAPAWGFFSSFLLLAF.TLVAALLGAAHRLGLFYQLMHKVDTAS.RHGGENVAAVLK
Retrocopy LRSRCQLMETTAAAAPAWGFFSSFLLLAFRTLVAALLGAAHRLGLFYQLMHKVDTASIRHGGENVAAVLK

Parental  AHGVRFLFTLVGGHISPLLVACEKLGIRVVDTRHEVTAVFAADAVARLTGTVGVAAVTAGPGLTNTVTAV
          AHGVRFLFTLVG.HISPLLVACEK..I.VVDT.HEVTAVFA.DAVARLTGT.GVAAVTAGPGLTN.VTAV
Retrocopy AHGVRFLFTLVGRHISPLLVACEKPDICVVDTHHEVTAVFATDAVARLTGTMGVAAVTAGPGLTNAVTAV

Parental  KNAQIAQSPVLLLGGAASTLLQNRGALQAIDQIALFRPLCKFCASVRRVRDIIPTLRAAMAAAQSGTPGP
          KNAQIAQSPVLLLGGAA.TLLQNRGALQA.DQIALFRPLCKFCASVRRVRDIIPTLRAAMAAAQSGTPGP
Retrocopy KNAQIAQSPVLLLGGAANTLLQNRGALQAVDQIALFRPLCKFCASVRRVRDIIPTLRAAMAAAQSGTPGP

Parental  VFVELPLDVLYPYFMVQKEMVPAKPPKGLMSRAVHWYLANSLANLFAGAWEPQPEGPLPLDIPQASPQQV
          V..ELPLDVLYPYFMVQKEMVP.KPPK..MS.AVHWYLAN.LAN.FAGAWE..PEGPLPLDIPQASPQQV
Retrocopy VIMELPLDVLYPYFMVQKEMVPGKPPKVVMSPAVHWYLANPLANPFAGAWELEPEGPLPLDIPQASPQQV

Parental  QRCVEILSRAKKPLMLIGSQALLPPTSSDKLRVAVETLGIPCFLAGMARGLLGRNHPLHFRQNRRAALKK
          Q.CVEI.S.AK.PLMLI.SQALLPPTS..KL.VAVE.LGIPCFLAGMARGLLGRNHPLHF.QNRRAALKK
Retrocopy Q*CVEI*SWAKRPLMLIRSQALLPPTSAGKLWVAVENLGIPCFLAGMARGLLGRNHPLHFQQNRRAALKK

Parental  ADVVVLAGAVCDFRLSYGRVLSRSSKIIVV
          ADVVVLAGAVC.FRLSYG.VLS.SSKIIVV
Retrocopy ADVVVLAGAVCHFRLSYGCVLSCSSKIIVV

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	14.35 RPM
ERP005899_muscle	0.00 RPM	122.89 RPM
SRP017611_brain	0.00 RPM	15.85 RPM
SRP017611_kidney	0.00 RPM	54.06 RPM
SRP017611_liver	0.00 RPM	89.86 RPM
SRP030211_testis	0.27 RPM	6.54 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1619 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1619 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1619 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	ENSBTAG00000015186	1 retrocopy	retro_btau_1619 ,
Tursiops truncatus	ENSTTRG00000015412	1 retrocopy	retro_ttru_247,