RetrogeneDB ID: retro_ogar_800

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873528.1:1834298..1835190(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACSM3
• Ensembl ID: ENSOGAG00000011552
• Aliases: None
• Description: acyl-CoA synthetase medium-chain family member 3 [Source:HGNC Symbol;Acc:10522]

Sequence

>retro_ogar_800
TCTCCATGGAGCCAGGGAGCATGTGTATTTTCACACTATTTATCCCATTTTGAGCCAATTTCCATCTTGCAAATGCTTTC
CAAGTTTCCTATCACAGTCTTCTGTACGGCACCAACTGCTTACTGAATGCTTATACACAATGATATGACCAGCTATAAGT
TCAAAAACTTAAAGCACTGTGTGAGCACTGGGGAACCAATCAATCCTGAAGTGATTGAACAATGGAGAAACAAGACTGGC
CTTGATATCTATGAAGGATATGGACGAACTGAAACGGTTCTAATCTGTGGAAATTTTAAGGGAATGAAAATTAAGCCTGG
CTCAATGGGAAAGCCTTCTCCAGCTTTTGATGTTAAGATTTTAGATGCACATGGCAATATTTTACCTCCTGGACAGGAAG
GAGATATTGGCATTCGAGTTCTACCTAACCGACCATTGGGTCTTTTTACTCACTATATAAATAATCCTTCAAAAACAGCT
TCAACTCTATGAGGCAATTTCTATATCACTGGGGACAGAGGGTATGTGGATAAAGATGGCTACTTCTGGTTTGTTGCAAG
AGCAGATGATATCATATTATCTTCTTGTTACCGAATTGGACCATTTGAAGTAGAAAGTACCCTAATTGAGCACCCTTCGG
TTGCAGAATCAGCTGTTGTCAGCAGTCCGGACTCCATCAGAGGAGAGGTAGTAAAGGCTTTTATTGTTCTGAATCCTGAT
TACAAGTTACACGATCAAGAACAACTTAAAAAGGAGATTCAGGAGCATGTTAAAAAAAACTACAGCACCTTAGAAACATC
CCAGAAAGGTAGAATTTATTCCAGAGCTGACAAAGACTGTCAGTGGGAAGATAAAAAGAAATGAACTGAGGAAGAAAGAA
TGGAAAACACTT

Alignment

ORF - retro_ogar_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.28 %
• Parental protein coverage: 50.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPWSQGACVFAHYLPHFEPTSILQTLSKFPITVFCTAPTAYRMLVHNDMTSYKFKNLKHCVSAGEPINPE
          SPWSQGACVF.HYL.HFEP.SILQ.LSKFPITVFCTAPTAY.ML.HNDMTSYKFKNLKHCVS.GEPINPE
Retrocopy SPWSQGACVFSHYLSHFEPISILQMLSKFPITVFCTAPTAY*MLIHNDMTSYKFKNLKHCVSTGEPINPE

Parental  VIEQWRNKTGLDIYEGYGQTETVLICGNFKGMKIKPGSMGKPSPAFDVKILDAHGNVLPPGQEGDIGIRV
          VIEQWRNKTGLDIYEGYG.TETVLICGNFKGMKIKPGSMGKPSPAFDVKILDAHGN.LPPGQEGDIGIRV
Retrocopy VIEQWRNKTGLDIYEGYGRTETVLICGNFKGMKIKPGSMGKPSPAFDVKILDAHGNILPPGQEGDIGIRV

Parental  LPNRPFGLFTHYVDNPSKTASTLRGNFYITGDRGYVDKDGYFWFVARADDIILSSGYRIGPFEVESALIE
          LPNRP.GLFTHY..NPSKTASTL.GNFYITGDRGYVDKDGYFWFVARADDIILSS.YRIGPFEVES.LIE
Retrocopy LPNRPLGLFTHYINNPSKTASTL*GNFYITGDRGYVDKDGYFWFVARADDIILSSCYRIGPFEVESTLIE

Parental  HPSVAESAVVSSPDPIRGEVVKAFIVLNPDYKLHDQEQLKKEIQEHV-KKTTAPYKYPRKVEFIPELPKT
          HPSVAESAVVSSPD.IRGEVVKAFIVLNPDYKLHDQEQLKKEIQEHV....TAP.K.PRKVEFIPEL.KT
Retrocopy HPSVAESAVVSSPDSIRGEVVKAFIVLNPDYKLHDQEQLKKEIQEHV>XXXTAP*KHPRKVEFIPELTKT

Parental  VSGKIKRNELRKKEWKTL
          VSGKIKRNELRKKEWKTL
Retrocopy VSGKIKRNELRKKEWKTL

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_800 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000011552	1 retrocopy	retro_ogar_800 ,