RetrogeneDB ID: retro_btau_1699

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:26785905..26786247(-)
• Located in intron of: ENSBTAG00000021667

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.22851
• Ensembl ID: ENSBTAG00000039732
• Aliases: None
• Description: protein Muted homolog [Source:RefSeq peptide;Acc:NP_001092345]

Sequence

>retro_btau_1699
GGCAAGAGTGGTGGCAAGAAGAAGGACTTGCTGGGAACCACAGGCTCACCAGTGCACCTCATCATCAAGGATCTTGGAGA
AATTCATTCAAGTCTATTAGATCATAAACCAGTTATCCACGGCAAAACTCATTATTTTTTGATAGAATTTGAAGAAAAAT
GTGGCCTTCGAGAAATGCAAGTTCTTGAAAATTTGAAGAATACGACCTATGAGACAAATGAACATACTCTTCTGAAGTGT
AGGGAAACAATGCAAGATAACTTAAACCAAGTTCTCCAGAGACTGCAACCAGCTACTGACTCAGTCTGTAGACTCCAACA
GAGGGAACAGGAGAGAAAAGAG

Alignment

ORF - retro_btau_1699 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.07 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGGGGKKKDSQGFTGSPAHLIIKDLGEIHSRLLDHRPVIQGETRYFVKEFEEKRGLREMRVLENLKNMIH
          G..GGKKKD..G.TGSP.HLIIKDLGEIHS.LLDH.PVI.G.T.YF..EFEEK.GLREM.VLENLKN...
Retrocopy GKSGGKKKDLLGTTGSPVHLIIKDLGEIHSSLLDHKPVIHGKTHYFLIEFEEKCGLREMQVLENLKNTTY

Parental  ETNEHTLPTCRATMQDSLNQVLQRLQAATDSVRRLQQREQERKK
          ETNEHTL..CR.TMQD.LNQVLQRLQ.ATDSV.RLQQREQERK.
Retrocopy ETNEHTLLKCRETMQDNLNQVLQRLQPATDSVCRLQQREQERKE

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	14.56 RPM
ERP005899_muscle	0.00 RPM	23.60 RPM
SRP017611_brain	0.09 RPM	14.89 RPM
SRP017611_kidney	0.00 RPM	29.52 RPM
SRP017611_liver	0.00 RPM	9.36 RPM
SRP030211_testis	0.01 RPM	11.50 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1699 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1699 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1699 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017324	1 retrocopy	retro_amel_1747,
Bos taurus	ENSBTAG00000039732	2 retrocopies	retro_btau_1699 , retro_btau_1747,
Monodelphis domestica	ENSMODG00000010026	1 retrocopy	retro_mdom_1483,
Oryctolagus cuniculus	ENSOCUG00000025755	2 retrocopies	retro_ocun_1051, retro_ocun_269,
Otolemur garnettii	ENSOGAG00000030827	1 retrocopy	retro_ogar_2470,
Ictidomys tridecemlineatus	ENSSTOG00000027342	3 retrocopies	retro_itri_1038, retro_itri_179, retro_itri_1901,