RetrogeneDB ID: retro_btau_1732

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:24094115..24094417(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM3
• Ensembl ID: ENSBTAG00000007363
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm3 [Source:UniProtKB/Swiss-Prot;Acc:Q32PE9]

Sequence

>retro_btau_1732
ATGGCAGACCGCATGGACCGGCAACAAACTACCAACACCATAGAAGAGCCCCTGGATCATCTCAGGCTCAGCCTGGATGA
GAAAATCTATGTGAAAATGAGAAACAACAGAGAACTTTGAGGCAGGTTACATGCTTACAATCAATATTTAAGCACAATAT
TGGGAAATATGGAAGAAACTGTGCAACTATAGAAAGTGAAGGAGAAGCATTTCAAGAGATATATAAATCAACAAAATGGA
ATATTCTGATGCTCTTTGTCTGGGGAGATGGTGTTGTGCTAGTGGTCCCACCATTTACAGTT

Alignment

ORF - retro_btau_1732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.57 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETV-TTIEIDEE
          MAD..D.QQTTNT.EEPLD..RLSLDE.IYVKMRN.REL.GRLHAY.Q.L..ILG..EETV..TIE...E
Retrocopy MADRMDRQQTTNTIEEPLDHLRLSLDEKIYVKMRNNREL*GRLHAYNQYLSTILGNMEETV<ATIESEGE

Parental  TYEEIYKSTKRNIPMLFVRGDGVVLVAPPLRV
          ...EIYKSTK.NI.MLFV.GDGVVLV.PP..V
Retrocopy AFQEIYKSTKWNILMLFVWGDGVVLVVPPFTV

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	20.69 RPM
ERP005899_muscle	0.00 RPM	21.12 RPM
SRP017611_brain	0.05 RPM	6.99 RPM
SRP017611_kidney	0.00 RPM	14.82 RPM
SRP017611_liver	0.00 RPM	9.29 RPM
SRP030211_testis	0.00 RPM	40.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1732 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1732 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1732 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007363	1 retrocopy	retro_btau_1732 ,
Callithrix jacchus	ENSCJAG00000016977	1 retrocopy	retro_cjac_54,
Cavia porcellus	ENSCPOG00000006671	1 retrocopy	retro_cpor_1445,
Dasypus novemcinctus	ENSDNOG00000018032	7 retrocopies	retro_dnov_1046, retro_dnov_135, retro_dnov_1728, retro_dnov_1818, retro_dnov_229, retro_dnov_230, retro_dnov_2408,
Echinops telfairi	ENSETEG00000016207	8 retrocopies	retro_etel_117, retro_etel_1678, retro_etel_1852, retro_etel_2131, retro_etel_472, retro_etel_521, retro_etel_598, retro_etel_833,
Homo sapiens	ENSG00000170860	5 retrocopies	retro_hsap_1045, retro_hsap_1654, retro_hsap_1839, retro_hsap_2286, retro_hsap_2986,
Gorilla gorilla	ENSGGOG00000010006	4 retrocopies	retro_ggor_104, retro_ggor_1699, retro_ggor_2068, retro_ggor_826,
Loxodonta africana	ENSLAFG00000023308	1 retrocopy	retro_lafr_1013,
Macaca mulatta	ENSMMUG00000023126	5 retrocopies	retro_mmul_1038, retro_mmul_1657, retro_mmul_1908, retro_mmul_554, retro_mmul_828,
Oryctolagus cuniculus	ENSOCUG00000011088	1 retrocopy	retro_ocun_126,
Oreochromis niloticus	ENSONIG00000000370	1 retrocopy	retro_onil_12,
Pongo abelii	ENSPPYG00000013402	4 retrocopies	retro_pabe_1366, retro_pabe_1936, retro_pabe_2475, retro_pabe_874,
Pan troglodytes	ENSPTRG00000014650	5 retrocopies	retro_ptro_1125, retro_ptro_1161, retro_ptro_1619, retro_ptro_2020, retro_ptro_712,
Rattus norvegicus	ENSRNOG00000008733	1 retrocopy	retro_rnor_1187,
Sus scrofa	ENSSSCG00000011601	6 retrocopies	retro_sscr_1134, retro_sscr_1140, retro_sscr_395, retro_sscr_396, retro_sscr_457, retro_sscr_64,
Tursiops truncatus	ENSTTRG00000011197	1 retrocopy	retro_ttru_601,