RetrogeneDB ID: retro_mmur_1315

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_4353:87849..88822(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHB
• Ensembl ID: ENSMICG00000006750
• Aliases: None
• Description: hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit [Source:HGNC Symbol;Acc:4803]

Sequence

>retro_mmur_1315
TTGATTGCCTCTGGCCAGTGTGATGTCATCGTGGCAGGTGGTGTAGAAGTTAATGTCCGATGTCCCTATTCCGTCATTCA
AGAAAAATGAAGAAAATGATGCTTGATCTCAATAAGGCCAAGACCTGGGCCAGAGACTGTCTTTAATCTCTAAATTCAGA
TTGAATTTCCTATCACCTGAGCTCCCTGCAGTGGCTGAGTTCTCTACCAGTGAGACCATGGGCCATTCTGCAGACCGACT
GGCTGCTGCCTTTGCTGTTTCTTGACTGGAGCAGGATGAACATGCACTGCGTTCTCACAGTCTGGCCAAGAAGGCACAGG
ATGAAGGGCTCCTTTCTGATGTTATACCCTTCAAAGTACCAGGAAAAGATACAGTTACCAAAGATAATGGTATCCGTCCT
TCCTCGCTGGAGCAGATGGCCAAACTAAAACCTGTATTCATCAAGCCCTATGGCACAGTGACAGCTGCAAATTCTTCTTT
CCTGACTGATGGCGCATCTGCAATGCTGATTATGGCAGAGGAAAAAGCTCTGGCCATGGGTTATAAGCCAAAGGCATATT
TGAGGGATTTTGTGTATGTGTCTCAGGATCCAAAAGATCAACTTTTACTTGGACCAACATATGCTACTCCAAAAGTTCTG
GAAAAGGCAGGATTGACCATGAATGATATTGACGCTTATGAATTTCACGAAGCTTTCTCAGGTCAAATTTTGGCTAATTT
TAAAGCCATGGATTCTGATTGGTTTGCACAAAACTACATGGGTAGAAAAACTAAGGTTGGAATGCCTCCTTTGGAGAAGT
TTAATAACTGGGGTGGATCACTGTCCCTGGGACACCCATTTGGAGCCACTGGCTGTCGGTTGGTCATGGCGGCTGCCAAC
AGATTGCGGAAGGAAGGAGGCCAGTATGGCTTAGTGGCTGCCTGTGCAGCAGGAGGACAGGGCCATGCCATGATAGTGGA
AGCTTATTCAAAA

Alignment

ORF - retro_mmur_1315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.64 %
• Parental protein coverage: 68.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LIASGQCDVIVAGGVE-LMSDVPI-RHSRKMRKMMLDLNKAKT-LGQRLSLISKFRLNFLSPELPAVAEF
          LIASGQCDVIVAGGVE.LMSDVPI.RHSRKM.KMMLDLNKAKT.LGQRLSLISKFRLNFLSPELPAVAEF
Retrocopy LIASGQCDVIVAGGVE>LMSDVPI>RHSRKMKKMMLDLNKAKT<LGQRLSLISKFRLNFLSPELPAVAEF

Parental  STSETMGHSADRLAAAFAVSRLEQDEYALRSHSLAKKAQDEGLLSDVIPFKVPGKDTVTKDNGIRPSSLE
          STSETMGHSADRLAAAFAVS.LEQDE.ALRSHSLAKKAQDEGLLSDVIPFKVPGKDTVTKDNGIRPSSLE
Retrocopy STSETMGHSADRLAAAFAVS*LEQDEHALRSHSLAKKAQDEGLLSDVIPFKVPGKDTVTKDNGIRPSSLE

Parental  QMAKLKPAFIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKAYLRDFVYVSQDPKDQLLLGPTY
          QMAKLKP.FIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKAYLRDFVYVSQDPKDQLLLGPTY
Retrocopy QMAKLKPVFIKPYGTVTAANSSFLTDGASAMLIMAEEKALAMGYKPKAYLRDFVYVSQDPKDQLLLGPTY

Parental  ATPKVLEKAGLTMNDIDAYEFHEAFSGQILANFKAMDSDWFAQNYMGRKTKEVTPPLEKFNYWGGSLSLG
          ATPKVLEKAGLTMNDIDAYEFHEAFSGQILANFKAMDSDWFAQNYMGRKTK...PPLEKFN.WGGSLSLG
Retrocopy ATPKVLEKAGLTMNDIDAYEFHEAFSGQILANFKAMDSDWFAQNYMGRKTKVGMPPLEKFNNWGGSLSLG

Parental  HPFGATGCRLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYSK
          HPFGATGCRLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYSK
Retrocopy HPFGATGCRLVMAAANRLRKEGGQYGLVAACAAGGQGHAMIVEAYSK

Legend:

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

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_1315 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1315 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002288	1 retrocopy	retro_amel_1473,
Canis familiaris	ENSCAFG00000029395	1 retrocopy	retro_cfam_2114,
Choloepus hoffmanni	ENSCHOG00000010050	3 retrocopies	retro_chof_122, retro_chof_1869, retro_chof_911,
Homo sapiens	ENSG00000138029	1 retrocopy	retro_hsap_4778,
Gorilla gorilla	ENSGGOG00000025829	1 retrocopy	retro_ggor_2976,
Microcebus murinus	ENSMICG00000006750	1 retrocopy	retro_mmur_1315 ,
Mus musculus	ENSMUSG00000059447	2 retrocopies	retro_mmus_1427, retro_mmus_1961,
Otolemur garnettii	ENSOGAG00000005444	1 retrocopy	retro_ogar_167,
Pongo abelii	ENSPPYG00000012582	1 retrocopy	retro_pabe_3718,
Pan troglodytes	ENSPTRG00000011733	1 retrocopy	retro_ptro_3180,
Tarsius syrichta	ENSTSYG00000003570	2 retrocopies	retro_tsyr_1316, retro_tsyr_1951,