RetrogeneDB ID: retro_btau_1182

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:37575177..37575612(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000022460
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSBTAG00000003770
• Aliases: None
• Description: 6-pyruvoyl tetrahydrobiopterin synthase [Source:RefSeq peptide;Acc:NP_001107009]

Sequence

>retro_btau_1182
ATGAACGGGGCAGGGTTGGGCCCTGGCTGGTGGGCGCGAGTGTCCCGCCTCGTCTCCTTCAGCGCGAGCCACCGCCTCCA
CAGCAAATCTCTTAGTAATGAAGAAAACTTGAAATTATTTGGGAAGTGCAACAACCCAAATGGCCATGGGCACAATTACA
AAGTTGTGGTAACAGTACATGGAGAGGTTGATCCTGTTACAGGAATGGTCATGAATTTGACTGACCTCAAAGAGTATATA
GAGGAGGCGATTATGAAGCCCCTTGATCATAAGAATCTGGATCTAGGTGTGCCGTATTTTGCAGACATTGTAAGCACAAC
AGAAAATGTAGCCGTTTATATCTGGGAAAACCTCCAGAAATTTCTTCCTGTGGGAGTTCTTTATAAAGTAAAAGTATATG
AAACCGACAATAATATTGTAGTCTATAAAGGAGAA

Alignment

ORF - retro_btau_1182 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGAGSGPRRRARVSRLVSFSATHRLHSKSLSNEENLKLFGKCNNPNGHGHNYKVVVTVHGEVDPVTGMV
          MNGAG.GP...ARVSRLVSFSA.HRLHSKSLSNEENLKLFGKCNNPNGHGHNYKVVVTVHGEVDPVTGMV
Retrocopy MNGAGLGPGWWARVSRLVSFSASHRLHSKSLSNEENLKLFGKCNNPNGHGHNYKVVVTVHGEVDPVTGMV

Parental  MNLTDLKKYMEEAIMKPLDHKNLDLDVPYFADIVSTTENVAVYIWENLQKFLPVGVLYKVKVYETDNNIV
          MNLTDLK.Y.EEAIMKPLDHKNLDL.VPYFADIVSTTENVAVYIWENLQKFLPVGVLYKVKVYETDNNIV
Retrocopy MNLTDLKEYIEEAIMKPLDHKNLDLGVPYFADIVSTTENVAVYIWENLQKFLPVGVLYKVKVYETDNNIV

Parental  VYKGE
          VYKGE
Retrocopy VYKGE

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	0.07 RPM	13.34 RPM
ERP005899_muscle	0.00 RPM	6.55 RPM
SRP017611_brain	0.05 RPM	11.33 RPM
SRP017611_kidney	0.00 RPM	8.48 RPM
SRP017611_liver	0.08 RPM	6.19 RPM
SRP030211_testis	0.01 RPM	13.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1182 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003968	3 retrocopies	retro_amel_1001, retro_amel_1480, retro_amel_691,
Bos taurus	ENSBTAG00000003770	3 retrocopies	retro_btau_1182 , retro_btau_1762, retro_btau_682,
Canis familiaris	ENSCAFG00000013915	2 retrocopies	retro_cfam_1386, retro_cfam_1859,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Felis catus	ENSFCAG00000024702	3 retrocopies	retro_fcat_1546, retro_fcat_212, retro_fcat_564,
Myotis lucifugus	ENSMLUG00000023388	1 retrocopy	retro_mluc_946,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Sorex araneus	ENSSARG00000001975	2 retrocopies	retro_sara_163, retro_sara_72,
Sus scrofa	ENSSSCG00000015040	1 retrocopy	retro_sscr_284,
Tursiops truncatus	ENSTTRG00000010526	1 retrocopy	retro_ttru_1710,
Vicugna pacos	ENSVPAG00000000061	1 retrocopy	retro_vpac_363,