RetrogeneDB ID: retro_btau_1249

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:7704852..7705326(-)
• Located in intron of: ENSBTAG00000005227

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME3
• Ensembl ID: ENSBTAG00000019918
• Aliases: None
• Description: None

Sequence

>retro_btau_1249
AAGGTACTAGCACTGCCCGGCGGCGAGGGACAGCTTCTGCGGAGCAACCAGCATCTGGTGGAGCTGATTGAGCGTGTAAA
GCCTGAGATCGAGCTGCTGAGAGAGAAATGCAACACGGTGCGGATGTGGGTGCAGCTGCTCATTCCGAAGGTGGAAGACG
GCAACAACTTCGGCGTGTCCATCCAGGAAGACACCGTGGACCAGCTGTGGACCGTGGAGAGCACAGCAGCCTCCTATCTA
CGCCGCTTCTCCACCTACTACAACACCAGGGCAAAGTTGGTATCAAAGATAGTGAAATATCCCCAGGTAGAAGATTATCG
CCGCACTGTAGCGGAGGTCGACGAAAATGAGTACCTGAGTGTGCGCCAGATCCTGCTCCATTTACGGAACCAGTATGCCA
CTTTGCATGATGTAATCCTCAAGAATATCGAGAAGATCAAGACCCCGCGGAGCACCAACACTGACAACCTTTAC

Alignment

ORF - retro_btau_1249 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.89 %
• Parental protein coverage: 61.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVFVMPNG---MLKSNQQLVDIIEKVKPEIRLLIEKCNTVKMWVQLLIPRIEDGNNFGVSIQEETVAELR
          KV...P.G....L.SNQ.LV..IE.VKPEI.LL.EKCNTV.MWVQLLIP..EDGNNFGVSIQE.TV..L.
Retrocopy KVLALPGGEGQLLRSNQHLVELIERVKPEIELLREKCNTVRMWVQLLIPKVEDGNNFGVSIQEDTVDQLW

Parental  TVESEAASYLDQISRYYITRAKLVSKIAKYPHVEDYRRTVTEIDEKEYISLRLIISELRNQYVTLHDMIL
          TVES.AASYL...S.YY.TRAKLVSKI.KYP.VEDYRRTV.E.DE.EY.S.R.I...LRNQY.TLHD.IL
Retrocopy TVESTAASYLRRFSTYYNTRAKLVSKIVKYPQVEDYRRTVAEVDENEYLSVRQILLHLRNQYATLHDVIL

Parental  KNIEKIKRPRSSNAETLY
          KNIEKIK.PRS.N...LY
Retrocopy KNIEKIKTPRSTNTDNLY

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	0.29 RPM	13.48 RPM
ERP005899_muscle	0.00 RPM	30.93 RPM
SRP017611_brain	0.00 RPM	37.82 RPM
SRP017611_kidney	0.18 RPM	36.45 RPM
SRP017611_liver	0.00 RPM	23.41 RPM
SRP030211_testis	17.10 RPM	88.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1249 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1249 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_245
Pan troglodytes	retro_ptro_212
Pongo abelii	retro_pabe_413
Oryctolagus cuniculus	retro_ocun_641
Sus scrofa	retro_sscr_784
Equus caballus	retro_ecab_827

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013688	2 retrocopies	retro_acar_118, retro_acar_37,
Bos taurus	ENSBTAG00000019918	2 retrocopies	retro_btau_1249 , retro_btau_941,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Callithrix jacchus	ENSCJAG00000013111	1 retrocopy	retro_cjac_2307,
Cavia porcellus	ENSCPOG00000012552	1 retrocopy	retro_cpor_1204,
Equus caballus	ENSECAG00000012620	2 retrocopies	retro_ecab_29, retro_ecab_827,
Homo sapiens	ENSG00000131467	1 retrocopy	retro_hsap_245,
Loxodonta africana	ENSLAFG00000013446	1 retrocopy	retro_lafr_725,
Mustela putorius furo	ENSMPUG00000010027	1 retrocopy	retro_mputfur_619,
Oryctolagus cuniculus	ENSOCUG00000015986	1 retrocopy	retro_ocun_641,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413,
Pan troglodytes	ENSPTRG00000009225	1 retrocopy	retro_ptro_212,
Sus scrofa	ENSSSCG00000017385	1 retrocopy	retro_sscr_784,
Ictidomys tridecemlineatus	ENSSTOG00000028833	1 retrocopy	retro_itri_153,