RetrogeneDB ID: retro_mmul_1235

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:52662207..52662709(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000022646
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSMMUG00000012930
• Aliases: None
• Description: None

Sequence

>retro_mmul_1235
ATGAACTGTCCAGCCCCTGTGGAGATCTCCTATGAGAACATGTATTTTCTGATAACTCACAACCCAACCAATGCTACTCT
CAACAAGTTCACAGAGGAACTTAAGAAGTATGGAGTGATGACTTTGGTTCAAGTTTGTGATGCTACCTATGATAAAGCTC
CAGTTGAAAAAGAAGGAATCCACGTTCTAGATTGGCCATTGGATGATGGAGCCCCACCCCCTAATCAGATAGTAGATGAT
TGGTTAAACCTGTTAAAAACCAAATTTCATGAAGAGCCAGGTTGCTCTGTTGCAGTGCATTGTGTTGCGGGATTGGGAAG
GGGCACCTGTGCTGGTTGCACTTGCTTTGATTGAATGTGGAATGAAGTACGAAGATGCAGTTCAGTTTATAAGACAAAAA
AGAAGGGGAGTGTTCCATTCCAAACAGCTGCTTTACTTGGAGAAATACCGACCTAAGATGCAATTACACTTCAGAAATAC
CAATGGGCATTGCTGTGTTCAG

Alignment

ORF - retro_mmul_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATLNKFT-ELQQIFSRTFMEFGDC---RAPVEKEGIHVLDWPFDDG
          MN.PAPVEISYENM.FLITHNPTNATLNKFT.EL......T.....D.....APVEKEGIHVLDWP.DDG
Retrocopy MNCPAPVEISYENMYFLITHNPTNATLNKFTEELKKYGVMTLVQVCDATYDKAPVEKEGIHVLDWPLDDG

Parental  APPPNQIVDDWLNLLKTKFREEPGCCVAVHCVAGLGR-APVLVALALIECGMKYEDAVQFIRQKRRGAFN
          APPPNQIVDDWLNLLKTKF.EEPGC.VAVHCVAGLGR.APVLVALALIECGMKYEDAVQFIRQKRRG.F.
Retrocopy APPPNQIVDDWLNLLKTKFHEEPGCSVAVHCVAGLGR>APVLVALALIECGMKYEDAVQFIRQKRRGVFH

Parental  SKQLLYLEKYRPKMRLRFRDTNGHCCVQ
          SKQLLYLEKYRPKM.L.FR.TNGHCCVQ
Retrocopy SKQLLYLEKYRPKMQLHFRNTNGHCCVQ

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	2.24 RPM	62.75 RPM
SRP007412_brain_prefrontal_cortex	2.06 RPM	41.17 RPM
SRP007412_cerebellum	1.68 RPM	37.07 RPM
SRP007412_heart	3.95 RPM	65.30 RPM
SRP007412_kidney	1.76 RPM	62.32 RPM
SRP007412_liver	1.90 RPM	26.56 RPM
SRP007412_testis	6.90 RPM	102.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1235 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 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	ENSMMUG00000002777	1 retrocopy	retro_mmul_1720,
Macaca mulatta	ENSMMUG00000012930	1 retrocopy	retro_mmul_1235 ,
Macaca mulatta	ENSMMUG00000019392	1 retrocopy	retro_mmul_1132,
Pan troglodytes	ENSPTRG00000000467	4 retrocopies	retro_ptro_1212, retro_ptro_562, retro_ptro_654, retro_ptro_727,