RetrogeneDB ID: retro_btau_1195

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:24139754..24140074(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGC134282
• Ensembl ID: ENSBTAG00000010465
• Aliases: None
• Description: None

Sequence

>retro_btau_1195
TTGGGTGCTGCAGGTGGAAAGATCAGCTGGCCGTGAACAGAGCTGAAGAAGCTGTTCAAGCAATGTCAAGTGTTGAACTG
GGAGTGGCAACTGAAACATCGGGTGGTCAGAGGTGTGATAGACAAAGGACTGATTACACGGCACTACCTCAAGTAGTGGG
CGTCCAGTGCATGTGCCAACATTACTCTGGGAAGAAATGCAGAAAACTCCTGCCACAGATCTGACTTGCCCAGAAAGAGA
AAGCAGGCATGGAAGCAGAAGCCCCTCCTAAGCCAACCAGGACTAGTGAACCACAGCCCAAATCAAAAAAGAAGACAGAA

Alignment

ORF - retro_btau_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.82 %
• Parental protein coverage: 88.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGAPSGKINRPRTELKKKLFKRRRVLNRERRLKHRVVGAVIDEGLITRHHLKKRASSARANITLSGK-KR
          .GA..GKI..P.TELKK.LFK...VLN.E..LKHRVV..VID.GLITRH.LK..ASSA.ANITL.G..K.
Retrocopy LGAAGGKISWP*TELKK-LFKQCQVLNWEWQLKHRVVRGVIDKGLITRHYLK*WASSACANITL-GR<KC

Parental  RKLLQQIRLAQKEKAAMEVEAPPKPTRTSDPQPRSKKKTK
          RKLL.QI.LAQKEKA.ME.EAPPKPTRTS.PQP.SKKKT.
Retrocopy RKLLPQI*LAQKEKAGMEAEAPPKPTRTSEPQPKSKKKTE

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	4.69 RPM
ERP005899_muscle	0.00 RPM	6.65 RPM
SRP017611_brain	0.00 RPM	8.04 RPM
SRP017611_kidney	0.00 RPM	7.47 RPM
SRP017611_liver	0.00 RPM	8.23 RPM
SRP030211_testis	0.01 RPM	44.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1195 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1195 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1195 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006512	1 retrocopy	retro_amel_1386,
Bos taurus	ENSBTAG00000010465	2 retrocopies	retro_btau_1195 , retro_btau_1799,
Canis familiaris	ENSCAFG00000015719	2 retrocopies	retro_cfam_1104, retro_cfam_757,
Felis catus	ENSFCAG00000025454	2 retrocopies	retro_fcat_1722, retro_fcat_773,
Macaca mulatta	ENSMMUG00000013949	4 retrocopies	retro_mmul_1186, retro_mmul_1541, retro_mmul_1785, retro_mmul_1981,
Mus musculus	ENSMUSG00000071653	2 retrocopies	retro_mmus_1809, retro_mmus_759,
Otolemur garnettii	ENSOGAG00000033103	1 retrocopy	retro_ogar_811,
Rattus norvegicus	ENSRNOG00000019701	4 retrocopies	retro_rnor_1066, retro_rnor_1955, retro_rnor_851, retro_rnor_883,
Sus scrofa	ENSSSCG00000023323	2 retrocopies	retro_sscr_1162, retro_sscr_1163,