RetrogeneDB ID: retro_ogar_3007

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873695.1:3448387..3449389(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACADM
• Ensembl ID: ENSOGAG00000007657
• Aliases: None
• Description: acyl-CoA dehydrogenase, C-4 to C-12 straight chain [Source:HGNC Symbol;Acc:89]

Sequence

>retro_ogar_3007
AATATACACATTCCATAGAGTTGTGGAGGTCTCAGACTTGGAACTTTTGATGCTTGTTTAATAACTGAAGAATTGGCTTA
TGGATGCACTGGGGTTCAGATTGCTATTGAAGCAAATTCTTTGGGACAAATGCCTGTTATTATTGCTGGAAATGATCAGC
AAAAAAAGAAGTATTAGGGGAGAATGACTAAAGAGCCATTGATGTGTGCCTACTGTGTAACAGATCCTGAGCAGGCTCTG
ATGTAGCTGGTTTGAAGACCAAAGCAGAAAAGAAAGGAGATGAGTATATTATTAATGGTCAGAAGATGTGCATAACCAAT
GGAGGAAAAGCTAATGGGTATTTTCTTACTGGCACGTTCTGATCCAGATCCTAAGGCTCCTGCTGGCAAAGCCTTTACTG
GGTTTATTGTGGAAGCAGATACCCCAGGAATACAGATTGGAAGAAAGGAATTAAACATGGGCCAGTGATGTTCAGATACT
AGAGGAATTGTCTTTGAAGATGTGAAAGTGCCTAAGGAAAATGTTTTAATTGGTGAAGGAGCTGGTTTCAAAATTGCAAT
GGGAGTTTTTGATAAAACCAGACCTCCAGTAGCAGCTGGTGCTGTTGGATTAGCACAAAGAGCTTTGGATGAAGCTACCA
AGTATGCCCTGGAAAGGAAAACTTTTGGAAAGCCAATTGTAGAGCACCAAGGGATAACATTTCTGCTGGCTGAAATGGCA
ATGAAAGATGAACTAGCTAGATTGAGTTACCAGAGAGCAGCCTGGAAGGTTGATTCTGGTCACTGAAATACCTGTTATGC
TTCTATTGCAAAGGCATTTGCTGGAGATATTGCAAATCAGGTAGCTACTGATGCTGTGCAGATTTTTGGAGGCAACGGAT
TTAATACAGAATATCCTGTAGAGAAACTAATGAGGGATGCCAAGATCTATCAGATTTATGAAAGTACTACACAAATTCAA
AGGCTTATTATAGCCTGAGAACACATTGGCAAGTATAAAAAC

Alignment

ORF - retro_ogar_3007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.18 %
• Parental protein coverage: 73.57 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NLNLILNFGGLGLGTFDACLITEELAYGCTGVQTAIEANSLGQMPIIIAGNDQQKKKYLGRLTEEPLMCA
          N.......GGL.LGTFDACLITEELAYGCTGVQ.AIEANSLGQMP.IIAGNDQQKKKY.GR.T.EPLMCA
Retrocopy NIHIP*SCGGLRLGTFDACLITEELAYGCTGVQIAIEANSLGQMPVIIAGNDQQKKKY*GRMTKEPLMCA

Parental  YCVTEPG-AGSDVAGLKTKAEKKGDEYIINGQKMWITNGGKANWY-FLLARSDPDPKAPAGKAFTGFIVE
          YCVT.P..AGSDVAGLKTKAEKKGDEYIINGQKM.ITNGGKAN.Y.FLLARSDPDPKAPAGKAFTGFIVE
Retrocopy YCVTDPE<AGSDVAGLKTKAEKKGDEYIINGQKMCITNGGKANGY>FLLARSDPDPKAPAGKAFTGFIVE

Parental  ADTPGIQIGRKELNMGQRCSDTRGIVFEDVRVPKENVLIGEGAGFKIAMGAFDKTRPPVAAGAVGLAQRA
          ADTPGIQIGRKELNMGQ.CSDTRGIVFEDV.VPKENVLIGEGAGFKIAMG.FDKTRPPVAAGAVGLAQRA
Retrocopy ADTPGIQIGRKELNMGQ*CSDTRGIVFEDVKVPKENVLIGEGAGFKIAMGVFDKTRPPVAAGAVGLAQRA

Parental  LDEATNYALERKTFGKPIIEHQGISFLLAEMAMKVELARLSYQRAAWEVDSGRRNTYYASIAKAFAGDIA
          LDEAT.YALERKTFGKPI.EHQGI.FLLAEMAMK.ELARLSYQRAAW.VDSG..NT.YASIAKAFAGDIA
Retrocopy LDEATKYALERKTFGKPIVEHQGITFLLAEMAMKDELARLSYQRAAWKVDSGH*NTCYASIAKAFAGDIA

Parental  NQVATDAVQIFGGNGFNTEYPVEKLMRDAKIYQIYEGTAQIQRLIIAREHIGKYKN
          NQVATDAVQIFGGNGFNTEYPVEKLMRDAKIYQIYE.T.QIQRLIIA.EHIGKYKN
Retrocopy NQVATDAVQIFGGNGFNTEYPVEKLMRDAKIYQIYESTTQIQRLIIA*EHIGKYKN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3007 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024240	1 retrocopy	retro_btau_1680,
Otolemur garnettii	ENSOGAG00000007657	1 retrocopy	retro_ogar_3007 ,
Otolemur garnettii	ENSOGAG00000015375	1 retrocopy	retro_ogar_2468,
Tarsius syrichta	ENSTSYG00000007164	1 retrocopy	retro_tsyr_371,