RetrogeneDB ID: retro_btau_1680

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:85047794..85048778(+)
• Located in intron of: ENSBTAG00000016844

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACADM
• Ensembl ID: ENSBTAG00000024240
• Aliases: None
• Description: Medium-chain specific acyl-CoA dehydrogenase, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q3SZB4]

Sequence

>retro_btau_1680
AGTTTTGGAGGTCTTGGACTTGGAACTTTTGATAGCTGTTTAATTTCTGAAGAATTGGCTTATGGATGTACAGGGGTTCA
GACTGCTATTGAAGCAAATTCTCTAGGGCAAATGCCTGTTATTATTGCTGGAAATGATCAACAACAAAAGAAATATTGGG
GGAGAATGACTGAGGAGCCATTAATGTGTGCCTATTGTGTAACAGAACCTGTAGCAGGCTCTGATGTAGCTGGTATAAAA
ACCAAAGCAGAAAAGAAAGGAGATGAGTATATTATTAATGGTCAGAAGACGTGGATCACCAATGGAGGAAAAGCTAATTG
GTATTTTTTATTGGCTCATTCTGATCCGGATCCTAAGGCTCCTGCTAGTAAAGCCTTTACTGGCTTTATTGTGGAAGCAG
ACACCCCAGGAGTACAGATTGGAAGAAAGGAATTAAATATGGGACAGCGATGTTCAGATACAAGAGGAATTGTCTTTGAA
GATGTGAGAGTGCCCAAGGAAAATGTTTTAATTGGTGAGGGAGCTGGTTTCAAAATTGCAATGGGAGCATTTGATAAAAC
CAGACCACCAGTAGCAGCTGCTGCTGTGGGACTAGCACAGAGAGCTTTGGATGAAGCTACCAAGTATGCCCTGGAGAGAA
AAACTTTTGGAAAGCTGCTTATAGAGCACCAAGGAATATCATTTTTGCTGGCTGAAATGGCAATGAAAGTTGAACTAGCT
AGATTGAGTTACCAGAGAGCAGCTTGGGAAGTTGATTCTGGTCGCCGAAATACCTATTATGCCTCTATTGCAAAGGCATA
TGCTGGAGATATCGCAAATCAGTTAGCTTCTGATGCTGTTCAGATTTTTGGAGGCAATGGATTTAATACTGAATATCCTG
TAGAAAAATTAATGAGAGATGCCAAGATCTATCAGATTTATGAAGGTACAGCACAAATTCAAAGGCTTATTATAGCCCGT
GAACACATTGGCAGGTATAAGAAG

Alignment

ORF - retro_btau_1680 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.78 %
• Parental protein coverage: 77.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SCGGLGLGTFDSCLISEELAYGCTGVQTAIEANSLGQMPVIIAGNDQQQKKYLGRMTEEPLMCAYCVTEP
          S.GGLGLGTFDSCLISEELAYGCTGVQTAIEANSLGQMPVIIAGNDQQQKKY.GRMTEEPLMCAYCVTEP
Retrocopy SFGGLGLGTFDSCLISEELAYGCTGVQTAIEANSLGQMPVIIAGNDQQQKKYWGRMTEEPLMCAYCVTEP

Parental  VAGSDVAGIKTKAEKKGDEYIINGQKMWITNGGKANWYFLLARSDPDPKAPASKAFTGFIVEADTPGVQI
          VAGSDVAGIKTKAEKKGDEYIINGQK.WITNGGKANWYFLLA.SDPDPKAPASKAFTGFIVEADTPGVQI
Retrocopy VAGSDVAGIKTKAEKKGDEYIINGQKTWITNGGKANWYFLLAHSDPDPKAPASKAFTGFIVEADTPGVQI

Parental  GRKELNMGQRCSDTRGIVFEDVRVPKENVLIGEGAGFKIAMGAFDKTRPPVAAAAVGLAQRALDEATKYA
          GRKELNMGQRCSDTRGIVFEDVRVPKENVLIGEGAGFKIAMGAFDKTRPPVAAAAVGLAQRALDEATKYA
Retrocopy GRKELNMGQRCSDTRGIVFEDVRVPKENVLIGEGAGFKIAMGAFDKTRPPVAAAAVGLAQRALDEATKYA

Parental  LERKTFGKLLIEHQGISFLLAEMAMKVELARLSYQRAAWEVDSGRRNTYYASIAKAYAGDIANQLASDAV
          LERKTFGKLLIEHQGISFLLAEMAMKVELARLSYQRAAWEVDSGRRNTYYASIAKAYAGDIANQLASDAV
Retrocopy LERKTFGKLLIEHQGISFLLAEMAMKVELARLSYQRAAWEVDSGRRNTYYASIAKAYAGDIANQLASDAV

Parental  QIFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRLIIAREHIGRYKK
          QIFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRLIIAREHIGRYKK
Retrocopy QIFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRLIIAREHIGRYKK

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	6.20 RPM	273.03 RPM
ERP005899_muscle	0.32 RPM	43.50 RPM
SRP017611_brain	0.37 RPM	27.86 RPM
SRP017611_kidney	2.49 RPM	293.16 RPM
SRP017611_liver	1.89 RPM	119.08 RPM
SRP030211_testis	0.09 RPM	18.14 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1680 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1680 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1680 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024240	1 retrocopy	retro_btau_1680 ,
Otolemur garnettii	ENSOGAG00000007657	1 retrocopy	retro_ogar_3007,
Tarsius syrichta	ENSTSYG00000007164	1 retrocopy	retro_tsyr_371,