RetrogeneDB ID: retro_mmur_337

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2469:149279..149803(-)
• Located in intron of: ENSMICG00000007893

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX3
• Ensembl ID: ENSMICG00000004602
• Aliases: None
• Description: Y box binding protein 3 [Source:HGNC Symbol;Acc:2428]

Sequence

>retro_mmur_337
GCGGAGGAGGAAGAAGAGAAAGGGAATGGCAGCAGTGAAAGATTTGAGCCCCCTGCCACTGACCGGCAGTTCTTTGGGGC
CCGGAATCAGCTGCGCCGCCCTCAGTACTGGCAGCGGCGGTTCCCGCCTTACCGCGTGGGACAAACCTTTGACCGTCGCT
CACGGGTCTTTCCCCGTCCCGACAGAATGCAAGCTGGTCAGATTGGAGAGAGTAAGGACCGGATCCCAGAGAGAGCACAA
CTTCAGAGACCGGTTCATCGAAATGCAACCTATCGCCCAAGGTACCATCGGGGACTTCTTCGCCCACGACCTGCCCCTGC
TGTTGAGGAGGCCGAAGATAAAGAGAATCAGCAAGCAGCCAATGGTCCAAACCAGCCATCTGCTCGCATGGATACCGGCG
TCCCTACAACTATAGGCGTCGCCCCGGTCCTCCTAACGTTCCCTCGCAAGATGGCAGAGAGACCAAGGCAGGTGACGCCC
CAACTGAGAAGCCCGCTCCTGCCACCGAGCAGAGCAGTGCTGAG

Alignment

ORF - retro_mmur_337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 63.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGEEEEEGSGSSEGFEPPATDRQFSGARNQLRRPQYRPQYRQRRFPPYHVGQTFDRRSRVFPHPNRMQAG
          A.EEEE.G.GSSE.FEPPATDRQF.GARNQLR....RPQY.QRRFPPY.VGQTFDRRSRVFP.P.RMQAG
Retrocopy AEEEEEKGNGSSERFEPPATDRQFFGARNQLR----RPQYWQRRFPPYRVGQTFDRRSRVFPRPDRMQAG

Parental  EIGEIKDGVPEGAQLQGPVHRNPTYRPRYRSRGPPRPRPAPAVGEAEDKENQQAANGPNQPSAR-RGYRR
          .IGE.KD..PE.AQLQ.PVHRN.TYRPRY..RG..RPRPAPAV.EAEDKENQQAANGPNQPSAR..GYRR
Retrocopy QIGESKDRIPERAQLQRPVHRNATYRPRYH-RGLLRPRPAPAVEEAEDKENQQAANGPNQPSAR<HGYRR

Parental  PYNYRRRPRPPNAPSQDGKETKAGDATTENPAPTTEQSSAE
          PYNYRRRP.PPN.PSQDG.ETKAGDA.TE.PAP.TEQSSAE
Retrocopy PYNYRRRPGPPNVPSQDGRETKAGDAPTEKPAPATEQSSAE

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_337 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_337 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 4 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002557	1 retrocopy	retro_etel_1898,
Microcebus murinus	ENSMICG00000004602	1 retrocopy	retro_mmur_337 ,
Microcebus murinus	ENSMICG00000014984	19 retrocopies	retro_mmur_1098, retro_mmur_1285, retro_mmur_1326, retro_mmur_1435, retro_mmur_1437, retro_mmur_1445, retro_mmur_1621, retro_mmur_199, retro_mmur_315, retro_mmur_413, retro_mmur_581, retro_mmur_640, retro_mmur_676, retro_mmur_679, retro_mmur_726, retro_mmur_837, retro_mmur_900, retro_mmur_919, retro_mmur_942,
Ictidomys tridecemlineatus	ENSSTOG00000002108	1 retrocopy	retro_itri_1884,