RetrogeneDB ID: retro_mmur_180

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_1599:242011..242334(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC4
• Ensembl ID: ENSMICG00000003864
• Aliases: None
• Description: ER membrane protein complex subunit 4 [Source:HGNC Symbol;Acc:28032]

Sequence

>retro_mmur_180
GGGTCCTTCAAACAGATTGCCATGACCTCTTCATCATGTACATGCAGGCAATACTATCTCCATCTTCCCTACTATGATGT
GTGTGTGATGGCTGGCAACCCATTCAGGCACTTATGGCCATTTCAGCCACTTTCAAAATGTTAGAAAGTTCAAGCCAGAA
GTTTCTTCAGGGTTTGGTCTATCTTATTGGGAACCTGATGGGTTTGGCTTTGGCTGTTTACAAGTGCCAGTCCATGGGAC
TGTTGCCTACACATGCATCAGACTGGTCAGCCTTCATTGAGCCTCCTGAGAGAATGGAGTTCAGTGGTGGAGGACTGCTT
TTG

Alignment

ORF - retro_mmur_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.27 %
• Parental protein coverage: 59.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GPLKQIPM-NLFIMYM-AGNTISIFPTMM-VCMMA-WRPIQALMAISATFKMLESSSQKFLQGLVYLIGN
          G..KQI.M..LFIMYM.AGNTISIFPTMM.VC.MA.W.PIQALMAISATFKMLESSSQKFLQGLVYLIGN
Retrocopy GSFKQIAM<DLFIMYM<AGNTISIFPTMM<VCVMA<WQPIQALMAISATFKMLESSSQKFLQGLVYLIGN

Parental  LMGLALAVYKCQSMGLLPTHASDWLAFIEPPERMEFSGGGLLL
          LMGLALAVYKCQSMGLLPTHASDW.AFIEPPERMEFSGGGLLL
Retrocopy LMGLALAVYKCQSMGLLPTHASDWSAFIEPPERMEFSGGGLLL

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_180 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_180 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005576	2 retrocopies	retro_chof_1859, retro_chof_254,
Dipodomys ordii	ENSDORG00000008407	2 retrocopies	retro_dord_387, retro_dord_581,
Echinops telfairi	ENSETEG00000001688	1 retrocopy	retro_etel_1631,
Felis catus	ENSFCAG00000001736	1 retrocopy	retro_fcat_759,
Macropus eugenii	ENSMEUG00000004615	1 retrocopy	retro_meug_1129,
Microcebus murinus	ENSMICG00000003864	2 retrocopies	retro_mmur_1313, retro_mmur_180 ,
Oryctolagus cuniculus	ENSOCUG00000006160	4 retrocopies	retro_ocun_1686, retro_ocun_395, retro_ocun_719, retro_ocun_817,
Ochotona princeps	ENSOPRG00000009190	1 retrocopy	retro_opri_605,
Pteropus vampyrus	ENSPVAG00000003824	1 retrocopy	retro_pvam_386,
Rattus norvegicus	ENSRNOG00000005719	1 retrocopy	retro_rnor_897,
Ictidomys tridecemlineatus	ENSSTOG00000000516	1 retrocopy	retro_itri_1008,