RetrogeneDB ID: retro_mmur_1548

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_8132:13863..14396(-)
• Located in intron of: ENSMICG00000016540

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSMICG00000006998
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_mmur_1548
TCCAATAAAACTACATTGCAAAAAATAGGAAAGAAACAGAATGAGAAGAGTAAAAAGATCGAAGAGGCAGAGCCTGAAGA
ATTTGTGACGGAAAAAGTACTGGATCGAAGTGTAGTAAATGGGAAAGTGGAGTGTTTCCTGCAGTGGAAGGGATTTGCAG
ATGCTGACAGTACTTGGGAACCTGAATTAAATTCAGATTGTCCAGAGTTAACTGAAGCATTTCTTAATTCTCAAAAAGCT
GGTAAAGAAAAAGATGGTACGAAAAGAAAATCTTTATCTGACAATGAATCTGACGATAGACAGCAAAGAAGAGACGCTGC
TGACAAAGCCAAGAGGCTTTGCCAGAGGTCCTGATCCTGAAAGAACAGTTGGCCCACGACAGCAGTGGGGATTAATGTTT
TCTAAGAAATGGAAAGACTCAGATGAGGCAGGTTTGGTGTGGCAAAAGAGGCAAATGTGAAGGTTCTCAAGTTGTGATTG
CTTTTTAAGAAGAGAAACTAACTTGGCATTCTTGTCCAGAAGATGAAGCTCAA

Alignment

ORF - retro_mmur_1548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.72 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPEL
          SNKTTLQK.GKKQN.KSKK.EEAEPEEFV.EKVLDR.VVNGKVE.FL.WKGF.DAD.TWEPE.N.DCPEL
Retrocopy SNKTTLQKIGKKQNEKSKKIEEAEPEEFVTEKVLDRSVVNGKVECFLQWKGFADADSTWEPELNSDCPEL

Parental  IEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAAD-KPRGFARGLDPERIIGATDSSGELMFLMK
          .EAFLNSQKAGKEKDGTKRKSLSD.ESDD......RDAAD.KPRGFARG.DPER..G.....G.LMF..K
Retrocopy TEAFLNSQKAGKEKDGTKRKSLSDNESDD--RQQRRDAAD>KPRGFARGPDPERTVGPRQQWG-LMFSKK

Parental  WKDSDEADLV-LAKEANMKC-PQIVIAFYEERLTWHSCPEDEAQ
          WKDSDEA.LV..AKEAN.K...Q.VIAF.EE.LTWHSCPEDEAQ
Retrocopy WKDSDEAGLV<VAKEANVKV<SQVVIAF*EEKLTWHSCPEDEAQ

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_1548 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1548 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 7 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006250	19 retrocopies	retro_dnov_1136, retro_dnov_1174, retro_dnov_1208, retro_dnov_1270, retro_dnov_1605, retro_dnov_2306, retro_dnov_2307, retro_dnov_2397, retro_dnov_2543, retro_dnov_2605, retro_dnov_2633, retro_dnov_321, retro_dnov_359, retro_dnov_385, retro_dnov_445, retro_dnov_772, retro_dnov_794, retro_dnov_833, retro_dnov_844,
Felis catus	ENSFCAG00000015224	6 retrocopies	retro_fcat_1005, retro_fcat_1103, retro_fcat_1485, retro_fcat_1519, retro_fcat_336, retro_fcat_473,
Microcebus murinus	ENSMICG00000006998	11 retrocopies	retro_mmur_1015, retro_mmur_1030, retro_mmur_1076, retro_mmur_1178, retro_mmur_1497, retro_mmur_1500, retro_mmur_1548 , retro_mmur_386, retro_mmur_421, retro_mmur_68, retro_mmur_685,
Microcebus murinus	ENSMICG00000009510	4 retrocopies	retro_mmur_1324, retro_mmur_178, retro_mmur_467, retro_mmur_999,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,