RetrogeneDB ID: retro_btau_601

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:47533028..47533337(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YKT6
• Ensembl ID: ENSBTAG00000000274
• Aliases: None
• Description: Synaptobrevin homolog YKT6 [Source:UniProtKB/Swiss-Prot;Acc:Q3T000]

Sequence

>retro_btau_601
CTGATTGTGGAGTGCTCTGCAAAAGATAGCCAAACTTCTGTGGAACAAGAATATCTGTGCTATGTCTTCGTGAGAAATGA
CAGTCTTGCAGAAGTGGTCATTGCTGACAGTGAACATCCATCCTGGGAGTCTTTTACCTTGCTAGAGAAGGTACTAGACG
AATTCTCCAAGCAGGTCCACAGGATAGACTGGCCAGTTGGATCCCCCTATACCATCCAGTACACAGGCCTGGACAGTCAC
CTCAGTAGACACCAGAACCCCCAAGAAGCTGACTCCATGACTAAAGTGCAGGCTGAACTGAATGAGACC

Alignment

ORF - retro_btau_601 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.85 %
• Parental protein coverage: 52.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIVERSAKGSRASVKEQEYLCHVYVRNDSLAGVVIADSEYPSRVAFTLLEKVLDEFSKQVDRIDWPTGSP
          LIVE.SAK.S..SV.EQEYLC.V.VRNDSLA.VVIADSE.PS...FTLLEKVLDEFSKQV.RIDWP.GSP
Retrocopy LIVECSAKDSQTSV-EQEYLCYVFVRNDSLAEVVIADSEHPSWESFTLLEKVLDEFSKQVHRIDWPVGSP

Parental  DTIRYSGLDSQLSRYQNPREADPMTKVQAELDET
          .TI.Y.GLDS.LSR.QNP.EAD.MTKVQAEL.ET
Retrocopy YTIQYTGLDSHLSRHQNPQEADSMTKVQAELNET

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	4.90 RPM
ERP005899_muscle	0.00 RPM	36.37 RPM
SRP017611_brain	0.00 RPM	20.92 RPM
SRP017611_kidney	0.00 RPM	28.45 RPM
SRP017611_liver	0.00 RPM	26.28 RPM
SRP030211_testis	0.02 RPM	53.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_601 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_601 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017618	1 retrocopy	retro_amel_967,
Bos taurus	ENSBTAG00000000274	1 retrocopy	retro_btau_601 ,
Canis familiaris	ENSCAFG00000002903	1 retrocopy	retro_cfam_740,
Choloepus hoffmanni	ENSCHOG00000011207	1 retrocopy	retro_chof_657,
Callithrix jacchus	ENSCJAG00000008053	2 retrocopies	retro_cjac_2394, retro_cjac_2492,
Dasypus novemcinctus	ENSDNOG00000015173	1 retrocopy	retro_dnov_1364,
Dipodomys ordii	ENSDORG00000016393	1 retrocopy	retro_dord_621,
Erinaceus europaeus	ENSEEUG00000001247	1 retrocopy	retro_eeur_267,
Felis catus	ENSFCAG00000014362	1 retrocopy	retro_fcat_1327,
Homo sapiens	ENSG00000106636	1 retrocopy	retro_hsap_3687,
Gorilla gorilla	ENSGGOG00000027036	1 retrocopy	retro_ggor_2493,
Macropus eugenii	ENSMEUG00000014769	1 retrocopy	retro_meug_2068,
Mustela putorius furo	ENSMPUG00000018200	2 retrocopies	retro_mputfur_141, retro_mputfur_165,
Mus musculus	ENSMUSG00000002741	1 retrocopy	retro_mmus_825,
Nomascus leucogenys	ENSNLEG00000003689	1 retrocopy	retro_nleu_2275,
Oryctolagus cuniculus	ENSOCUG00000002981	1 retrocopy	retro_ocun_15,
Pongo abelii	ENSPPYG00000017595	1 retrocopy	retro_pabe_3022,
Pan troglodytes	ENSPTRG00000019141	1 retrocopy	retro_ptro_2500,
Sus scrofa	ENSSSCG00000016750	1 retrocopy	retro_sscr_1063,
Tursiops truncatus	ENSTTRG00000006052	2 retrocopies	retro_ttru_1320, retro_ttru_417,