RetrogeneDB ID: retro_btau_915

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:6355836..6356278(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDNEP1
• Ensembl ID: ENSBTAG00000019443
• Aliases: CTDNEP1, DULLARD
• Description: CTD nuclear envelope phosphatase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q1RMV9]

Sequence

>retro_btau_915
GTAATAAACAAACATCCCTTCCGGTTTTTTGTACATAAGAGGCCCCATGTGGATTTCTTCTTAGAAGTGGTGAGCCAGTG
GTAGGAGTTGGTGGTGTTCACAACAATTCATGGAGATGTATGGCTCTGCTGTGGCAGATAAACTGGATAATAGCAGAAGC
ATTCTCAAGAGGAGATACTACAGACAGCACCGCACTTTGGAATGGGGCAGCTACATCAAGGACCTCTCTGCAGTCCACAG
TGACCTCTCCAGCGTTGTGATCCTGGATAACTCCCCAGGGGCTTACAGGAGCCATCCAGACAATGCCATCCCCATCAAAT
CCTGGTTCAGTGATCTCAGTGATACCACCCTTCTCAACCTGATTCCAGTGCTGGATGCCCTCAGGTTCACCGCTGTTGTT
TGTTCTGTGCTGAGCCGAAACCTTCACCAACATAGGCCCTGG

Alignment

ORF - retro_btau_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 60.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VIDKHPVRFFVHKRPHVDFFLEVVSQWYELVVFTAS-MEIYGSAVADKLDNSRSILKRRYYRQHCTLELG
          VI.KHP.RFFVHKRPHVDFFLEVVSQW.ELVVFT...ME.YGSAVADKLDNSRSILKRRYYRQH.TLE.G
Retrocopy VINKHPFRFFVHKRPHVDFFLEVVSQW*ELVVFTTI>MEMYGSAVADKLDNSRSILKRRYYRQHRTLEWG

Parental  SYIKDLSVVHSDLSSIVILDNSPGAYRSHPDNAIPIKSWFSDPSDTALLNLLPMLDALRFTADVRSVLSR
          SYIKDLS.VHSDLSS.VILDNSPGAYRSHPDNAIPIKSWFSD.SDT.LLNL.P.LDALRFTA.V.SVLSR
Retrocopy SYIKDLSAVHSDLSSVVILDNSPGAYRSHPDNAIPIKSWFSDLSDTTLLNLIPVLDALRFTAVVCSVLSR

Parental  NLHQHRLW
          NLHQHR.W
Retrocopy NLHQHRPW

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	11.54 RPM
ERP005899_muscle	0.00 RPM	53.21 RPM
SRP017611_brain	0.00 RPM	38.05 RPM
SRP017611_kidney	0.00 RPM	45.64 RPM
SRP017611_liver	0.00 RPM	21.14 RPM
SRP030211_testis	0.02 RPM	70.66 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_915 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_915 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915 ,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,