RetrogeneDB ID: retro_btau_1246

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:114025933..114027237(+)
• Located in intron of: ENSBTAG00000026181

Retrocopy information

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

Parental gene information

• Parental gene symbol: BYSL
• Ensembl ID: ENSBTAG00000010101
• Aliases: None
• Description: Bystin [Source:UniProtKB/Swiss-Prot;Acc:Q5E9N0]

Sequence

>retro_btau_1246
ATGCCCAAGTTCAAGGCGGCCCGCGGGGCCGGGGGTCAGGAAAAGCATGCACCGCTGGCCGAGCAGATCCTGGCTGGGGA
CGCGGTGCGGGCAGGAACCCGAGAAAAACGGCGGGGTCGCGGAACCGGAGACGAGGAGGAAGAGTACGTGGGGCCCCGGC
TGACCCGACAGATTTTGCAGCAAGCGCGGCAGCAGCAAGAGGAGCTCAAGGCAGAGCATGGGAGCGGGGACAGACCCGCG
GTGCCGCGGGAGCGCGCTATGCGGCTTGATCCAGGAGTGCGGCAGGATGGATCAGATGACGAGGAGTGGCCCACCCTGGA
GAAGGCTGCCACAACGGCAGGGCCGGGCTAGCAGGCGGAGGTGGTCGTGGACCCCGAGGATGAGCGTGCCCTTGAGATGT
TCATGAACCAGAACCCTCCTGCCAGGCGCACCCTGGCTGACATCATCATGGAGCAGTTAACTGAGAAGCAGACGAAGTCG
AAACGGTCATGTCCGAGGTCTCAGGCTTCCCTGTGCCCCAGCTGGACCCCCGCGTCCTAGAGGTCTACAGAGGGGTTCGG
GAGGTGTTGTCTAAGTACCGCAGTGGGAAACTGCCCAAGGCATTTAAGATCATCCCTGCCCTCTCCAACTGGGAGCAGAT
CCTCTACGTCACAGAGCCTGAGGCCTGGACCGCTGCTGCCATGTACCAAGCCACAAGGATTTTTGCCTCTAACTTAAAGG
AACGGATGGCCCAGCGCTTCTATAACCTGGTTCTGCTCCCCCGGGTATGAGATGACATTGCTGAGTACAAACGACTCAAC
TTCCACCTCTACATGGCCCTGAAGAAGGCCCTGTTCAAGCCTGGAGCCTGGTTTAAAGGCATCCTGATCCCGCTGTGCGA
GTCGGGCACCTGTACCCTCCTGGAAGCCATCATCGTGGGCAGCATCATCACCAAGTGCTCCATCCCCGTGCTGCACTCCA
GTGCAGCCATGCTGAAAATTGCAGAGATGGAGTACAGCGGGGCCAACAGCATTTTCCTGTGGCTGCTGCTGGACAAGAAG
TACGCACTGCCCTACCGAGTGCTGGACGCCCTGGTCTTCCACTTCCTGGGCTTCTGGACAGAGAAGCGTGAGCTGCCCGT
GCTCTGGCACCAGTGCCTGTTGACTTTGGTCCAGCGCTACAAGGCCGACCTAGCCACGGAGCAGAAGGAGGCCCTCCTGG
AACTGCTCCGGCTGCAGCCCCACCCCCAGCTGTCCCCGGAGATCAGGCGTGAGTTGCAGAGTGCCGTCCCCCGAGATGTA
GAAGATGTTCCCGTCACCATGGAG

Alignment

ORF - retro_btau_1246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.64 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKFKAARGAGVQEKHAPLAEQILAGDAVRAGTREKRRGRGTGDEEEEYVGPRLTRRILQQARQQQEELE
          MPKFKAARGAG.QEKHAPLAEQILAGDAVRAGTREKRRGRGTGDEEEEYVGPRLTR.ILQQARQQQEEL.
Retrocopy MPKFKAARGAGGQEKHAPLAEQILAGDAVRAGTREKRRGRGTGDEEEEYVGPRLTRQILQQARQQQEELK

Parental  AEHGSGDRPAVPRERTTRLGPGVPQDGSDDEEWPTLEQAAARAGPGYQAEVVVDPEDERAIEMFMNQNPP
          AEHGSGDRPAVPRER..RL.PGV.QDGSDDEEWPTLE.AA..AGPG.QAEVVVDPEDERA.EMFMNQNPP
Retrocopy AEHGSGDRPAVPRERAMRLDPGVRQDGSDDEEWPTLEKAATTAGPG*QAEVVVDPEDERALEMFMNQNPP

Parental  ARRTLADIIMEKLTEKQT-EVETVMSEVSGFPVPQLDPRVLEVYRGVREVLSKYRSGKLPKAFKIIPALS
          ARRTLADIIME.LTEKQT.EVETVMSEVSGFPVPQLDPRVLEVYRGVREVLSKYRSGKLPKAFKIIPALS
Retrocopy ARRTLADIIMEQLTEKQT<EVETVMSEVSGFPVPQLDPRVLEVYRGVREVLSKYRSGKLPKAFKIIPALS

Parental  NWEQILYITEPEAWTAAAMYQATRIFASNLKERMAQRFYNLVLLPRVRDDIAEYKRLNFHLYMALKKALF
          NWEQILY.TEPEAWTAAAMYQATRIFASNLKERMAQRFYNLVLLPRV.DDIAEYKRLNFHLYMALKKALF
Retrocopy NWEQILYVTEPEAWTAAAMYQATRIFASNLKERMAQRFYNLVLLPRV*DDIAEYKRLNFHLYMALKKALF

Parental  KPGAWFKGILIPLCESGTCTLREAIIVGSIITKCSIPVLHSSAAMLKIAEMEYSGANSIFLRLLLDKKYA
          KPGAWFKGILIPLCESGTCTL.EAIIVGSIITKCSIPVLHSSAAMLKIAEMEYSGANSIFL.LLLDKKYA
Retrocopy KPGAWFKGILIPLCESGTCTLLEAIIVGSIITKCSIPVLHSSAAMLKIAEMEYSGANSIFLWLLLDKKYA

Parental  LPYRVLDALVFHFLGFRTEKRELPVLWHQCLLTLVQRYKADLATEQKEALLELLRLQPHPQLSPEIRREL
          LPYRVLDALVFHFLGF.TEKRELPVLWHQCLLTLVQRYKADLATEQKEALLELLRLQPHPQLSPEIRREL
Retrocopy LPYRVLDALVFHFLGFWTEKRELPVLWHQCLLTLVQRYKADLATEQKEALLELLRLQPHPQLSPEIRREL

Parental  QSAVPRDVEDVPVTME
          QSAVPRDVEDVPVTME
Retrocopy QSAVPRDVEDVPVTME

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	0.79 RPM	2.02 RPM
ERP005899_muscle	1.74 RPM	10.82 RPM
SRP017611_brain	0.05 RPM	6.90 RPM
SRP017611_kidney	0.59 RPM	9.84 RPM
SRP017611_liver	0.45 RPM	6.72 RPM
SRP030211_testis	1.15 RPM	7.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1246 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1246 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010101	1 retrocopy	retro_btau_1246 ,
Choloepus hoffmanni	ENSCHOG00000011476	1 retrocopy	retro_chof_1615,
Macropus eugenii	ENSMEUG00000000759	2 retrocopies	retro_meug_1365, retro_meug_608,
Oryctolagus cuniculus	ENSOCUG00000017567	1 retrocopy	retro_ocun_514,