RetrogeneDB ID: retro_btau_1123

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 27:19025324..19025597(+)
• Located in intron of: ENSBTAG00000010355

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSBTAG00000002332
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm5 [Source:UniProtKB/Swiss-Prot;Acc:Q2HJH0]

Sequence

>retro_btau_1123
ATGGCAGCTAATTTGACCACTAACCCGTTGTAGCTGCTTCCTCTAGATCTTGTGGACAAGTGGATAGGATCAAGAATTCA
CATTGAGATGAAGAGTGATGAGGAGACTGTTGGTATACTTCTGGGATTTGGTGACTTTGTCAATATGGTATTGGAAGATG
TCACTGAATTTGAAATCATACCAGAAGGAAGAAGAATTACTAAATTAGATCCAATTTTTCTAAAGGGAAATAATATACCA
ATGCTGGTTCCTGGAGGACAAGGACCTGAAATA

Alignment

ORF - retro_btau_1123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANATTNPSQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVNMVLEDVTEFEITPEGRRITKLD
          MAAN.TTNP..LLPL.LVDK.IGSRIHI.MKSD.E.VG.LLGF.DFVNMVLEDVTEFEI.PEGRRITKLD
Retrocopy MAANLTTNPL*LLPLDLVDKWIGSRIHIEMKSDEETVGILLGFGDFVNMVLEDVTEFEIIPEGRRITKLD

Parental  QILLNGNNITMLVPGGEGPEV
          .I.L.GNNI.MLVPGG.GPE.
Retrocopy PIFLKGNNIPMLVPGGQGPEI

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	13.70 RPM
ERP005899_muscle	0.11 RPM	6.28 RPM
SRP017611_brain	0.32 RPM	6.49 RPM
SRP017611_kidney	0.00 RPM	8.59 RPM
SRP017611_liver	0.00 RPM	3.32 RPM
SRP030211_testis	0.20 RPM	10.20 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1123 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1123 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1123 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002332	3 retrocopies	retro_btau_1012, retro_btau_1123 , retro_btau_1313,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Loxodonta africana	ENSLAFG00000029579	3 retrocopies	retro_lafr_1000, retro_lafr_368, retro_lafr_922,
Mus musculus	ENSMUSG00000091625	4 retrocopies	retro_mmus_1568, retro_mmus_423, retro_mmus_826, retro_mmus_837,
Nomascus leucogenys	ENSNLEG00000015268	1 retrocopy	retro_nleu_179,
Otolemur garnettii	ENSOGAG00000013892	3 retrocopies	retro_ogar_2727, retro_ogar_3062, retro_ogar_881,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Pteropus vampyrus	ENSPVAG00000009786	1 retrocopy	retro_pvam_1410,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Tupaia belangeri	ENSTBEG00000004876	11 retrocopies	retro_tbel_1043, retro_tbel_1107, retro_tbel_1217, retro_tbel_1323, retro_tbel_1549, retro_tbel_1865, retro_tbel_2203, retro_tbel_2908, retro_tbel_2956, retro_tbel_3330, retro_tbel_4335,
Tursiops truncatus	ENSTTRG00000004237	3 retrocopies	retro_ttru_1521, retro_ttru_1585, retro_ttru_874,