RetrogeneDB ID: retro_meug_2

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_8964:89346..89868(+)
• Located in intron of: ENSMEUG00000005824

Retrocopy information

• Ensembl ID: ENSMEUG00000005842
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSMEUG00000002037
• Aliases: None
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_meug_2
ATGGCTCAAGTGAACCACCCAGCTCCTGTAGAAATCACCTACAAGAAGATGAGGTTCCTTATTACACACAATCCAACCAA
TGCAGCCTTAAACAAATTTATAGAGGAACTCAAGAAGTATGGAGTTACCACAGTTGTAAGAGTATGTGAAGCTACTTATG
ACACAACCCTCTTGGAGAAAGAAGGAATCCAGGTTCTGGATTGGCCATTTGATGATGGAGCACCACCATCCAAACAGATT
GTTGATGACTGGCTAAACCTCGTGAAAACTAAATATCGTGAAGAACCTGGCTGCTACATTGCTGTTCACTGCACTGCAGG
TCTTGGGAGATCTCCAGTGCTCGTTGCTCTTGCACTAATCGAAAGAGGAATGAAGTATGAAGATGTAGTGCCATTCATCA
GACAAAAACGTCGTGGAGCCTTTAACAGCAAGCAACTTCTTTACTTGGAGAAATATCGTCCTAAAATGCGGCTGCGTTTC
AAAGACTCAGATGGTCATAGAAACACGTGTTGCATTCAGTAA

Alignment

ORF - retro_meug_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFTEELKKYGVTTLVRVCDATYDKAPVEKE-IQVLDWPFDDG
          .N.PAPVEI.Y..MRFLITHNPTNA.LNKF.EELKKYGVTT.VRVC.ATYD....EKE.IQVLDWPFDDG
Retrocopy VNHPAPVEITYKKMRFLITHNPTNAALNKFIEELKKYGVTTVVRVCEATYDTTLLEKEGIQVLDWPFDDG

Parental  APPPNQIVDDWLNLLKSKFREEPGCCVAVHCVAGLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAFNS
          APP..QIVDDWLNL.K.K.REEPGC..AVHC.AGLGR.PVLVALALIE.GMKYED.V.FIRQKRRGAFNS
Retrocopy APPSKQIVDDWLNLVKTKYREEPGCYIAVHCTAGLGRSPVLVALALIERGMKYEDVVPFIRQKRRGAFNS

Parental  KQLLYLEKYRPKMRLRFRDTNGH---CCVQ
          KQLLYLEKYRPKMRLRF.D..GH...CC.Q
Retrocopy KQLLYLEKYRPKMRLRFKDSDGHRNTCCIQ

Legend:

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

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_2 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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 6 parental genes, and 13 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,
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,