RetrogeneDB ID: retro_mmur_163

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_153:3364..4140(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSMICG00000016578
• Aliases: None
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_mmur_163
ATGGCCCACCTGCGGGCCTGTGAAGTCCGGCAGCTGCTGCACAACAAGTTCGTAGTCGTCATGGGGGACTCGATCCAGCG
CGCCGTGTACAAGGACCTGGTGCTCCTGCTGCAGAAGGACTGCCTGCTCTCTTCCAGGCAGCTGAAGGCCAAGGGCGAGC
TGAGCTTCGAGCGCGACGTGCTGCTGGAGGGCGGCAGGTGGGGCCGCATGCACAACGGCACGCACTACCGCGAGGTGCGC
CAGTTCTGCGCCGGCCACCACCTGGTGCGCTTCTACTTCCTCACACGCGCGTACTCGCAGTACGTCGAGGACGTTCTGGA
AGAGCTGCAGGCTGGCGAGCACACCCCGGACGTGGTGGTCTTGAACTCCTGCCTCTGGGACGTCTCCAGGTACGGCCGCG
ACTTCCGCAGGAGCTACTGCGGGGACCTGGAGAGCCTGTTCGGGCGCCTGGCGCGGGTGCTGCCCGAGACCTGCCTCCTG
GTGTGGGAACACGGCCATGCCGGTGGCGGAGACCGTGTCGGGGGGCTTCCTTCCGCCTGAGCGCTGGCCCAGCCGCGCCC
GCCTGCGCAGGACGTGCTGGAGGCCAACTTCTACAGCGCCGCGAGGCGGGCAGGCATGGCTTCGACGTGCTGAACCTACA
TTTCCATTTCCGCCATGCCGGGCAGCACCGGCAGCGAGACGGCGTGCACTGGGACGAATGGGCGCACCGACACCTCTCGA
TGCTGCTGCTGGCCCACCTGGCGGACGCCTGGGGCGTGGAGCTCCCCTGTCGCGAA

Alignment

ORF - retro_mmur_163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.94 %
• Parental protein coverage: 57.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGEL
          M.H..A.EV.QLLHNKFVV..GDSIQRAVYKDLVLLLQKD.LL...QLKAKGELSFE.D.L..GG..G..
Retrocopy MAHLRACEVRQLLHNKFVVVMGDSIQRAVYKDLVLLLQKDCLLSSRQLKAKGELSFERDVLLEGGRWGRM

Parental  HNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYGP-APDLVIINSCLWDLSRYGRCSMES
          HNGT.YREVRQFC...GHHLVRFYFLTR.YS.Y.EDVLEEL..G...PD.V..NSCLWD.SRYGR....S
Retrocopy HNGTHYREVRQFC--AGHHLVRFYFLTRAYSQYVEDVLEELQAGEHTPDVVVLNSCLWDVSRYGRDFRRS

Parental  YRENLQRVFVRMDQVLPDSCLLVW-NMAMPLGERVTGGFLLPELQPLAGSLRR-DVVEGNFYSATL-AGD
          Y...L...F.R...VLP..CLLVW.N.AMP..E.V.GGFL.PE..P....LRR.DV.E.NFYSA...AG.
Retrocopy YCGDLESLFGRLARVLPETCLLVW>NTAMPVAETVSGGFLPPERWPSRARLRR<DVLEANFYSAAR<AGR

Parental  HCFDVLDLHFHFRHAVQHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPKRD
          H.FDVL.LHFHFRHA.QHR.RDGVHWD..AHRHLS.LLL.H.ADAWGVELP.R.
Retrocopy HGFDVLNLHFHFRHAGQHRQRDGVHWDEWAHRHLSMLLLAHLADAWGVELPCRE

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_163 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_163 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163 , retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,