RetrogeneDB ID: retro_btau_399

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:33026830..33027228(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOHB
• Ensembl ID: ENSBTAG00000019235
• Aliases: None
• Description: Protein mago nashi homolog 2 [Source:UniProtKB/Swiss-Prot;Acc:Q0VC92]

Sequence

>retro_btau_399
GACTTATGTCTGCATTACTGCATGGGTCACAACGGCAAGTTTAGCTTTGAATTCCTAGAGTCTAAGTTTTGACCTGATGG
AAATCAAGATATGCCAATAGCAGTGATTATAAAAATTATGTCATGATCAGAAAACAAGCTTATGTACATAAAAGTGTGAT
GGAGAAACTGAAGGGAATAGCTGATGACATTGAAATTCCCAAAGAGGATGATGCTTTTTGGCCTCCTCCCAACCAAGTAC
AGCAGCAGAAGCTTGAAATCATCATTGGAGATGAACACATTTCTTTCGCAAAATCAAAAATTGGTTCCCTTATTAGTGTC
AATCAATCCAAGGATCCAGAAAGCTTATGAGTATTTTATCATCTTCCCTCGGACCTGAAGTGTTTGCTCTACGGTCTT

Alignment

ORF - retro_btau_399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.15 %
• Parental protein coverage: 89.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFYLRYYVGHKGKFGHEFLEFEFRPDG-KLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKE
          D..L.Y..GH.GKF..EFLE..F.PDG.K.RYAN.S.YKN.VMIRK.AYVHKSVME.LK.I.DD.EI.KE
Retrocopy DLCLHYCMGHNGKFSFEFLESKF*PDG<KSRYANSSDYKNYVMIRKQAYVHKSVMEKLKGIADDIEIPKE

Parental  DDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSL
          DDA.WPPP..V..Q.LEI.IGDEHISF..SKIGSLI.VNQSKDPE.L.VFY.L..DLKCL...L
Retrocopy DDAFWPPPNQVQQQKLEIIIGDEHISFAKSKIGSLISVNQSKDPESL*VFYHLPSDLKCLLYGL

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	7.21 RPM
ERP005899_muscle	0.00 RPM	6.18 RPM
SRP017611_brain	0.05 RPM	1.78 RPM
SRP017611_kidney	0.00 RPM	6.10 RPM
SRP017611_liver	0.00 RPM	1.81 RPM
SRP030211_testis	0.04 RPM	8.15 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_399 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019235	1 retrocopy	retro_btau_399 ,
Choloepus hoffmanni	ENSCHOG00000004382	1 retrocopy	retro_chof_1730,
Dasypus novemcinctus	ENSDNOG00000005997	4 retrocopies	retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi	ENSETEG00000016591	3 retrocopies	retro_etel_1022, retro_etel_1566, retro_etel_2147,
Macropus eugenii	ENSMEUG00000001782	1 retrocopy	retro_meug_324,
Myotis lucifugus	ENSMLUG00000003527	2 retrocopies	retro_mluc_1039, retro_mluc_2484,
Macaca mulatta	ENSMMUG00000005082	1 retrocopy	retro_mmul_1246,
Monodelphis domestica	ENSMODG00000000462	1 retrocopy	retro_mdom_424,
Ochotona princeps	ENSOPRG00000000548	2 retrocopies	retro_opri_1171, retro_opri_308,
Sus scrofa	ENSSSCG00000000635	1 retrocopy	retro_sscr_971,
Tursiops truncatus	ENSTTRG00000001272	2 retrocopies	retro_ttru_515, retro_ttru_647,