RetrogeneDB ID: retro_btau_23

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:36063964..36064471(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000002943
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BT.41720
• Ensembl ID: ENSBTAG00000038020
• Aliases: None
• Description: None

Sequence

>retro_btau_23
ATGGCTGACAGTGGCAGAACGCCTCAGGCCCGGGCTCTCCTGCAGCAGTGCCTGCACGCCCGGCTGCAAGTACGCCCGGC
CGAGGGGGACGTCGAGGCCGAATGGGTGGAGGTTCAAAGAGGATTAGCGATCTACGTGTGCTTTTTCAAGGGAGCTGATA
AAGAACTTCTTCCCAAAATGGTTAATACACTGTTAAATGTGAAATTAAGTGAAACAGAAAATGGCAAGCACGTCTCTATA
TTGGATCTACCTGGCAACATTCTTATCATCCCTCAAGCCACCCTTGGGGGTAGAGTAAAAGGAAGAAGCATGCAGTATCA
CTGTAACTCTGGAAAAGAAGAGGGATTAGAACTTTATTCCCAATTTGTGAATCTCTGTAAAAAAGAATTAGCTGCTAATA
GCAAGTGTGCTGAAGCTGGGGTTGTTGTGAAACACGGTACTTACGGCAATAGGCAGGTGTTAAAGCTCGACACCAATGGA
CCGTACACACACCTAATTGAGTTTTGA

Alignment

ORF - retro_btau_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.4 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADSGRTPQARALLQQCLHARLQVRPAEGDVEAEWVEVQRGLVIYVCFFKGADKELLPKMVNTLLNVKLS
          MADSGRTPQARALLQQCLHARLQVRPAEGDVEAEWVEVQRGL.IYVCFFKGADKELLPKMVNTLLNVKLS
Retrocopy MADSGRTPQARALLQQCLHARLQVRPAEGDVEAEWVEVQRGLAIYVCFFKGADKELLPKMVNTLLNVKLS

Parental  ETENGKHVSILDLPGNILIIPQATLGGRVKGRSMQYHCNSGKEEGLELYSQFVNLCKKELAANSKCAEAG
          ETENGKHVSILDLPGNILIIPQATLGGRVKGRSMQYHCNSGKEEGLELYSQFVNLCKKELAANSKCAEAG
Retrocopy ETENGKHVSILDLPGNILIIPQATLGGRVKGRSMQYHCNSGKEEGLELYSQFVNLCKKELAANSKCAEAG

Parental  VVVKHGTYGNRQVLKLDTNGPYTHLIEF
          VVVKHGTYGNRQVLKLDTNGPYTHLIEF
Retrocopy VVVKHGTYGNRQVLKLDTNGPYTHLIEF

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	0.36 RPM
ERP005899_muscle	0.05 RPM	1.74 RPM
SRP017611_brain	0.05 RPM	0.46 RPM
SRP017611_kidney	0.06 RPM	1.42 RPM
SRP017611_liver	0.08 RPM	0.83 RPM
SRP030211_testis	0.01 RPM	0.92 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_23 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_23 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015731	1 retrocopy	retro_amel_696,
Bos taurus	ENSBTAG00000038020	1 retrocopy	retro_btau_23 ,
Mustela putorius furo	ENSMPUG00000001065	1 retrocopy	retro_mputfur_1052,
Rattus norvegicus	ENSRNOG00000006727	1 retrocopy	retro_rnor_1521,
Ictidomys tridecemlineatus	ENSSTOG00000025562	1 retrocopy	retro_itri_504,
Tursiops truncatus	ENSTTRG00000003788	3 retrocopies	retro_ttru_1617, retro_ttru_1832, retro_ttru_718,