RetrogeneDB ID: retro_btau_134

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 21:60886044..60886971(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000024311
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BT.105682
• Ensembl ID: ENSBTAG00000012279
• Aliases: None
• Description: L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase precursor [Source:RefSeq peptide;Acc:NP_001193406]

Sequence

>retro_btau_134
ATGGTTCTCCTCGCCTGGCGACTCTGCGTGCTGCCGGCGATGGAGGGCGTGCGCTGGGCCTTTCCCTGTGGCACGTGGCT
GCCGAACCGCGTCGAATGGCTGCTAGCTGTGCGATCGATCCAGCCCGAGGAGAAGGAACGCATTGGCCAGTTCGTCTTCG
CCCAGGACGCTAAGGCCGCCCTGGCTGGTCGTCTGATGATAAGGAAATTAGTTGCAGAGAAATTGAATATACCTTGGAAT
AATATTCGTTTGCAAAGAACTGCAAAAGGAAAACCAGTTCTTGCAAAAGACTCATTGAATCCTTACCCCAATTTCAACTT
TAACATCTCTCATCAAGGAGACTATGCTGTACTTGCTGCAGAATCTGAGCTACAAGTTGGAATTGATATAAGGAAGACTA
GTTTTCCAGGTCGTGGTTCAATTCCAGAATTTTTTCATATTATGAAAAGAAAGTTTACTGACAAAGAATGGGAAACAATC
AGAAGCTTTAAGGATGAATGGACTCAGCTGGATATGTTTTATAGGAATTGGGCACTGAAAGAAAGCTTCATAAAAGCAAT
AGGTGTTGGATTAGGATTTGAATTGCAACGGCTTGAATTCGATATATCCCCGTTAAACCTGGATATAGGCCAAGTTTATA
AAGAAACACGTTTATTTTTGGATGGAGAAGAAGAAAAAGAATGGGCATTTGAGGAAAGCAAAATAGATGAGCACCATTTT
GTTGCAGTAGCTCTTAGGAAACCCAATGGATCTAGACATCAGAATGTTACATCTCAAGATGATTCTAAAGCAACCCAGAG
GCAGTTTACTATTCTCACCTTTAATGATTTAATATCATCTGCAGTTCCTATGACCCCTGAAGATCCATTTTGGGACTGTT
TTTGCTTTACAGAAGAGATTTCAATAAGAAATGGTACAAAGTCATGA

Alignment

ORF - retro_btau_134 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLLAWRLCVLPAMEGVRWAFPCGTWLPSRAEWLLAVRSIQPEEKERIGQFVFARDAKAALAGRLMIRKL
          MVLLAWRLCVLPAMEGVRWAFPCGTWLP.R.EWLLAVRSIQPEEKERIGQFVFA.DAKAALAGRLMIRKL
Retrocopy MVLLAWRLCVLPAMEGVRWAFPCGTWLPNRVEWLLAVRSIQPEEKERIGQFVFAQDAKAALAGRLMIRKL

Parental  VAEKLNIPWNNIRLQRTAKGKPVLAKDSLNPYPNFNFNISHQGDYAVLAAESELQVGIDIMKTSFPGRGS
          VAEKLNIPWNNIRLQRTAKGKPVLAKDSLNPYPNFNFNISHQGDYAVLAAESELQVGIDI.KTSFPGRGS
Retrocopy VAEKLNIPWNNIRLQRTAKGKPVLAKDSLNPYPNFNFNISHQGDYAVLAAESELQVGIDIRKTSFPGRGS

Parental  IPEFFHIMKRKFTDKEWETIRSFKDEWTQLDMFYRNWALKESFIKAIGVGLGFELQRLEFDISPLNLDIG
          IPEFFHIMKRKFTDKEWETIRSFKDEWTQLDMFYRNWALKESFIKAIGVGLGFELQRLEFDISPLNLDIG
Retrocopy IPEFFHIMKRKFTDKEWETIRSFKDEWTQLDMFYRNWALKESFIKAIGVGLGFELQRLEFDISPLNLDIG

Parental  QVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVALRKPNGSRHQNVTSQDDSKATQRQFTILTFNDLISS
          QVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVALRKPNGSRHQNVTSQDDSKATQRQFTILTFNDLISS
Retrocopy QVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVALRKPNGSRHQNVTSQDDSKATQRQFTILTFNDLISS

Parental  AVPMTPEDPSFWDCFCFTEEISIRNGTKS
          AVPMTPEDP.FWDCFCFTEEISIRNGTKS
Retrocopy AVPMTPEDP-FWDCFCFTEEISIRNGTKS

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	6.78 RPM
ERP005899_muscle	0.11 RPM	15.89 RPM
SRP017611_brain	0.87 RPM	17.54 RPM
SRP017611_kidney	0.12 RPM	12.74 RPM
SRP017611_liver	0.23 RPM	4.08 RPM
SRP030211_testis	0.43 RPM	39.61 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_134 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_134 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012279	1 retrocopy	retro_btau_134 ,
Echinops telfairi	ENSETEG00000004248	2 retrocopies	retro_etel_1231, retro_etel_1503,
Myotis lucifugus	ENSMLUG00000016238	4 retrocopies	retro_mluc_1361, retro_mluc_1362, retro_mluc_1363, retro_mluc_479,
Mus musculus	ENSMUSG00000025894	1 retrocopy	retro_mmus_2827,
Oryctolagus cuniculus	ENSOCUG00000000231	1 retrocopy	retro_ocun_379,
Ictidomys tridecemlineatus	ENSSTOG00000000268	1 retrocopy	retro_itri_1438,
Tarsius syrichta	ENSTSYG00000005102	1 retrocopy	retro_tsyr_338,