RetrogeneDB ID: retro_amel_1484

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193482.1:422467..422740(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSAMEG00000017806
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_amel_1484
GTTTTTGATAAATGGTTAAAACTTGTAAAAAATAAATTTCATGAAGATCCTGGTTCCTGTATAGAGGTTCGCTGTGCTGC
GGATCTTGGGAGAGCTCCAGTGTTGGTTGCCTGAGCATTAAATGAAGGTGGAATGAAATATGACGGTGCAGTACAACTCA
TAAGACAAAGGCAGTATGGAGCTTTTAACAGCAAGAAACTTTTGTATTTGGAGAAGTATCATCCTACAGTGTACTTGCCC
CTCAGAAATGTCAGCTACAACTGTTTCATTCAA

Alignment

ORF - retro_amel_1484 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.34 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IVDDWLNLLKTKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNSKQLLYL
          ..D.WL.L.K.KF.E.PG.C..V.C.A.LGRAPVLVA.AL.E.GMKY..AVQ.IRQ...GAFNSK.LLYL
Retrocopy VFDKWLKLVKNKFHEDPGSCIEVRCAADLGRAPVLVA*ALNEGGMKYDGAVQLIRQRQYGAFNSKKLLYL

Parental  EKYRPKMRLRVRDTNGHCCVQ
          EKY.P...L..R.....C..Q
Retrocopy EKYHPTVYLPLRNVSYNCFIQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1484 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1484 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002438	3 retrocopies	retro_amel_1102, retro_amel_1344, retro_amel_1590,
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,
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,