RetrogeneDB ID: retro_btau_1393

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:84319430..84319836(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSCR6
• Ensembl ID: ENSBTAG00000036019
• Aliases: None
• Description: None

Sequence

>retro_btau_1393
GAGGAGGCTGTCAGAGCCCGGGAGGCACGGGGCTGTGTCTGTCACTGCGCCAGGGACGGTGCCCGGGGACCACTGCCCCT
GCGCGGGCCCGAGAGCCGTTTGCATGAAGACCCTGGATCCTGACCCCTCAGGATGCTGAACCCACCAGAACTGGAAGTGA
GCCTGAGCCAGGGGGTGAACAACAAACCTTTGGTTTGAAGGGGCCTTGAGGTTTCAGCATCCTGAAAGACTTCAGCTACC
CATTTCTAAGTGTCAAAAGTATCTGCAGAGTCCCAGGGAGAAGGTGTCAGCCAGTTTCCCAATGCGAGCCACCATTCAGT
TCTACAACAATGAGTAGCAGGAGGAAGACACCCAGCCCTCCCACCCCCAGTTCGAGGAGGCCCAGAAAGAAAGAGCAGAG
ACAGGT

Alignment

ORF - retro_btau_1393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.52 %
• Parental protein coverage: 75.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EAAAGAPEERGRVCHCVGDGPRGP-PAPRGPESQTPWRPWTLTPQEAEPTRTGSELEPAGDQETFGSKG-
          E.A..A.E.RG.VCHC..DG.RGP..AP.........RPW.LTPQ.AEPTRTGSE.EP.G.Q.TFG.KG.
Retrocopy EEAVRAREARGCVCHCARDGARGP<TAPARAREPFA*RPWILTPQDAEPTRTGSEPEPGGEQQTFGLKG<

Parental  AFGFQHPVRLYLPISKRQEYLQSSGEKVLASFPVQATIHFYNDESESEEELEEDTQLSALQREEVADG
          A..FQHP.RL.LPISK.Q.YLQS..EKV.ASFP..ATI.FYN.E...E.......Q....Q.E....G
Retrocopy ALRFQHPERLQLPISKCQKYLQSPREKVSASFPMRATIQFYNNE*QEEDTQPSHPQFEEAQKERAETG

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	0.00 RPM
ERP005899_muscle	0.00 RPM	0.11 RPM
SRP017611_brain	0.00 RPM	0.14 RPM
SRP017611_kidney	0.00 RPM	0.18 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.00 RPM	0.06 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1393 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1393 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036019	1 retrocopy	retro_btau_1393 ,
Homo sapiens	ENSG00000183145	1 retrocopy	retro_hsap_1407,
Gorilla gorilla	ENSGGOG00000006091	1 retrocopy	retro_ggor_1091,
Nomascus leucogenys	ENSNLEG00000004521	1 retrocopy	retro_nleu_1423,
Pongo abelii	ENSPPYG00000011408	1 retrocopy	retro_pabe_1163,
Pan troglodytes	ENSPTRG00000013896	1 retrocopy	retro_ptro_964,