RetrogeneDB ID: retro_mmur_1509

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_7203:29930..30583(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC13
• Ensembl ID: ENSMICG00000002401
• Aliases: None
• Description: SEC13 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:10697]

Sequence

>retro_mmur_1509
GTAATTAACACTGTGGACACCTCCCATGAGGACATGATTCACGATGAACAGATGGACTACCAAGGCACCTGCCTCGCAAC
CTGCTCATCAGACAGGTCCGTCCAAATCTCTGACCTGCGCAACGGAGGCCAGATCCTTATTGCCGACCTCAGGGGTCATG
AAGGTCCCATGTGGCAAGTGGCCTGGGCCCACCCCATGTACGGCAATATCCTGGCATCCTGCTCCTATGACCGGAAAGTC
ATTATCTGTAAAGAAGAAAACAGCACCCGGGAGAAGACCCGTGAGCAATCAGGACACAAGTTCTCAGTAAACTCTGTGTG
CTGGGCCCCTACGACCATGGCCTGCTCCTGGCCTGTGGGAGTTCGGGTGGGGCCATCTCCCCGCTGGCCTACACTGGGGG
AAGACCAGTGGGAAGTGAAGATCAACCACACTCGTGCTATTTGCTACAATGCTGTCAGTGGGGCCCCTGCTGTTGTACCT
GGAAGCCTCATAGTCCAGCCGTCAGGACAGAAACCCAATTACATTAAGAAGTTGGCATGAGGTAGCTGTGACAACCTTAT
CAAGCTGTGGGGGAGGAGGAGGATGGCCAGTGGAAGGAGGAGTAGAAGCTGGAAGTGCACAGGGACTGGGTCTGAGGCGT
GGCCTGGGCCCCT

Alignment

ORF - retro_mmur_1509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.18 %
• Parental protein coverage: 67.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMYGNI
          VINTVDTSHEDMIHD.QMDY.GT.LATCSSDRSV.I.D.RNGGQILIADLRGHEGP.WQVAWAHPMYGNI
Retrocopy VINTVDTSHEDMIHDEQMDYQGTCLATCSSDRSVQISDLRNGGQILIADLRGHEGPMWQVAWAHPMYGNI

Parental  LASCSYDRKVIIWKEENGTWEKTHEHSGHDSSVNSVCWA-PHDYGLILACGSSDGAISLLTYT-GEGQWE
          LASCSYDRKVII.KEEN.T.EKT.E.SGH..SVNSVCWA.P.D.GL.LACGSS.GAIS.L.YT.GE.QWE
Retrocopy LASCSYDRKVIICKEENSTREKTREQSGHKFSVNSVCWA<PYDHGLLLACGSSGGAISPLAYT>GEDQWE

Parental  VKKINNAHAIGCNAVSWAPAVVPGSLIDQPSGQKPNYIKKFASGGCDNLIKLW-KEEKDRQRKEEQKLEA
          V.KIN...AI..NAVS.APAVVPGSLI.QPSGQKPNYIKK.A.G.CDNLIKLW..EE.D.Q.KEE.KLE.
Retrocopy V-KINHTRAICYNAVSGAPAVVPGSLIVQPSGQKPNYIKKLA*GSCDNLIKLW<GEEEDGQWKEE*KLEV

Parental  HSDWVRDVAWAP
          H.DWV..VAWAP
Retrocopy HRDWV*GVAWAP

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_1509 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1509 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509 ,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,