RetrogeneDB ID: retro_mmur_338

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_248:559016..559273(+)
• Located in intron of: ENSMICG00000010076

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSMICG00000001424
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_mmur_338
GATTGGCCGTTGGACGATGGTACCCTGCCATCTAACCAGGATGTTGATGACTGGGTATGTCTTGCAAAAATGAAGTTTCT
CAAAGAACCTGGTTGTTGTATTGCTGTCATCGTGTTGCAGGTCTTGGGAGAGCTCTAGTGTTTGTTGCCCTAGCATTAAT
TGAAGATAGAGTGTAGTATGAAGATGCAGTAAAGTTCATAAGACAAAACTGGAGTGTAAACTTTAAAAGCAAGCAATTTT
TGCACTTGGAGAAGTAT

Alignment

ORF - retro_mmur_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 51.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DWPFDDGAPPPNQIVDDWLNLLKTKFREEPGCCVAV-HCVAGLGRAPVLVALALIECGMKYEDAVQFIRQ
          DWP.DDG..P.NQ.VDDW..L.K.KF..EPGCC.AV.H.VAGLGRA.V.VALALIE....YEDAV.FIRQ
Retrocopy DWPLDDGTLPSNQDVDDWVCLAKMKFLKEPGCCIAV<HRVAGLGRALVFVALALIEDRV*YEDAVKFIRQ

Parental  KRRGAFNSKQLLYLEKY
          .....F.SKQ.L.LEKY
Retrocopy NWSVNFKSKQFLHLEKY

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_338 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_338 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017806	1 retrocopy	retro_amel_1484,
Choloepus hoffmanni	ENSCHOG00000010834	1 retrocopy	retro_chof_2029,
Macropus eugenii	ENSMEUG00000002037	1 retrocopy	retro_meug_2,
Microcebus murinus	ENSMICG00000001424	5 retrocopies	retro_mmur_1393, retro_mmur_1475, retro_mmur_338 , retro_mmur_822, retro_mmur_910,
Microcebus murinus	ENSMICG00000006858	4 retrocopies	retro_mmur_269, retro_mmur_349, retro_mmur_642, retro_mmur_889,
Macaca mulatta	ENSMMUG00000012930	1 retrocopy	retro_mmul_1235,
Pan troglodytes	ENSPTRG00000000467	4 retrocopies	retro_ptro_1212, retro_ptro_562, retro_ptro_654, retro_ptro_727,