RetrogeneDB ID: retro_btau_1238

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:100068431..100068749(+)
• Located in intron of: ENSBTAG00000000094

Retrocopy information

• Ensembl ID: ENSBTAG00000048006
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NENF
• Ensembl ID: ENSBTAG00000000759
• Aliases: None
• Description: Neudesin [Source:UniProtKB/Swiss-Prot;Acc:Q1JQA5]

Sequence

>retro_btau_1238
GGCCCTGGTCAGGCAGATGCCACACCCTACCAGCTGGGGCCCCTGATGCAACTCTTCATCGAGGAGGAGTTGGCCCGCCC
TGGAGGGGAGGAAGATCTGCCAGAATACATGGCAGTGAAGGCAGTGGTGTTCGATGTCACCTCCAGAAAGGAGTTGTATG
GAGAAGGAGCACTCAGCGGTGTCTTGACCAAGAAGAACTCCACCACAGGGGTGACCAGGTTGTCTTTAGATCCTGCAGAC
TTCACCCATGACACTATAGGCCTCATGGCCCAGGAGCTGGAGCCCCCATATGACATTTTCACCAGAGTGTACACAGCC

Alignment

ORF - retro_btau_1238 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.49 %
• Parental protein coverage: 62.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAGQAPR-PAERGPPVRLFTEEELARYGGEEEDQPIYMAVKGVVFDVTSGKEFYGRGAPYNALTGKDSTR
          G.GQA...P...GP...LF.EEELAR.GGEE.D.P.YMAVK.VVFDVTS.KE.YG.GA....LT.K.ST.
Retrocopy GPGQADATPYQLGPLMQLFIEEELARPGGEE-DLPEYMAVKAVVFDVTSRKELYGEGALSGVLTKKNSTT

Parental  GVAKMSLDPADLTHDTTGLTAEELESLDDVFTRVYKA
          GV...SLDPAD.THDT.GL.A.ELE...D.FTRVY.A
Retrocopy GVTRLSLDPADFTHDTIGLMAQELEPPYDIFTRVYTA

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	8.58 RPM
ERP005899_muscle	0.00 RPM	54.21 RPM
SRP017611_brain	0.14 RPM	10.55 RPM
SRP017611_kidney	0.00 RPM	36.93 RPM
SRP017611_liver	0.00 RPM	13.67 RPM
SRP030211_testis	0.22 RPM	16.97 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1238 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1238 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_379
Pan troglodytes	retro_ptro_295
Pongo abelii	retro_pabe_328
Macaca mulatta	retro_mmul_490

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001341	1 retrocopy	retro_amel_836,
Bos taurus	ENSBTAG00000000759	1 retrocopy	retro_btau_1238 ,
Dasypus novemcinctus	ENSDNOG00000003399	1 retrocopy	retro_dnov_1256,
Felis catus	ENSFCAG00000031796	1 retrocopy	retro_fcat_1171,
Homo sapiens	ENSG00000117691	2 retrocopies	retro_hsap_3288, retro_hsap_379,
Gorilla gorilla	ENSGGOG00000025197	1 retrocopy	retro_ggor_830,
Macaca mulatta	ENSMMUG00000002142	2 retrocopies	retro_mmul_2064, retro_mmul_490,
Mus musculus	ENSMUSG00000037499	1 retrocopy	retro_mmus_3309,
Nomascus leucogenys	ENSNLEG00000002893	1 retrocopy	retro_nleu_1354,
Ochotona princeps	ENSOPRG00000014204	2 retrocopies	retro_opri_127, retro_opri_775,
Pongo abelii	ENSPPYG00000000236	2 retrocopies	retro_pabe_2717, retro_pabe_328,
Pan troglodytes	ENSPTRG00000001961	2 retrocopies	retro_ptro_2224, retro_ptro_295,
Sus scrofa	ENSSSCG00000015597	1 retrocopy	retro_sscr_393,
Ictidomys tridecemlineatus	ENSSTOG00000022293	2 retrocopies	retro_itri_1876, retro_itri_340,
Tarsius syrichta	ENSTSYG00000001880	3 retrocopies	retro_tsyr_1189, retro_tsyr_411, retro_tsyr_549,