RetrogeneDB ID: retro_mmul_49

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:85370926..85371598(-)
• Located in intron of: ENSMMUG00000003462

Retrocopy information

• Ensembl ID: ENSMMUG00000029538
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: HDAC3
• Ensembl ID: ENSMMUG00000012588
• Aliases: None
• Description: histone deacetylase 3 [Source:RefSeq peptide;Acc:NP_001253426]

Sequence

>retro_mmul_49
ATGTATGAAGTCGGGGCAGAGAGTGGCCACTACTACTGTCTGAATGTGCCCCTGCGGGATGGCATTGATGACCAGAGTTA
CAAATACCTTTTCCAGCCAGTTATCAACCAGGTAATGGACTTCTACCAACCCACATGCATTGTGCTCCAGTGTGGAGCTG
ACTCTCTGGGCTGTGATCGATTGGGCTGCTTTAACCTCAGCATCCGAGGGCATGGGGAATGTGTCGAATATGTCAAGAGC
TTCAATATCCCTCTACTGGTGCTGGGTGGTGGTGGTTATACTGTCCGAAATGTTGCCCGCTGCTGGACATATGAGACATC
GCTGCTGGTAGAAGAGGCCATTAGTGAGGAGCTTCCCTATAGTGAATACTTCGAGTACTTTGCCCCAGACTTCACACTTC
ATCCAGATGTCAGCACCCGCATCGAGAATCAGAACTCACGCCAGTATCTGGACCAGATCCGCCAGACAATCTTTGAAAAC
CTGAAGATGCTGAACCATGCACCTAGTGTCCAGATTCATGACGTGCCTGCAGACCTCCTGACCTATGACAGGACTGATGA
GGCTAATGCGGAGGACAGGGGTCCTGAGGAGAACTATAGCAGGCCAGAGGCACCCAATGAGTTCTGTGATGGAGACCATA
ACAACGACAAGGAAAGCGATGTGGAGATTTAA

Alignment

ORF - retro_mmul_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.86 %
• Parental protein coverage: 60.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYEVGAESGRYYCLNVPLRDGIDDQSYKHLFQPVINQVVDFYQPTCIVLQCGADSLGCDRLGCFNLSIRG
          MYEVGAESG.YYCLNVPLRDGIDDQSYK.LFQPVINQV.DFYQPTCIVLQCGADSLGCDRLGCFNLSIRG
Retrocopy MYEVGAESGHYYCLNVPLRDGIDDQSYKYLFQPVINQVMDFYQPTCIVLQCGADSLGCDRLGCFNLSIRG

Parental  HGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTR
          HGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTR
Retrocopy HGECVEYVKSFNIPLLVLGGGGYTVRNVARCWTYETSLLVEEAISEELPYSEYFEYFAPDFTLHPDVSTR

Parental  IENQNSRQYLDQIRQTIFENLKMLNHAPSVQIHDVPADLLTYDRTDEADAEERGPEENYSRPEAPNEFYD
          IENQNSRQYLDQIRQTIFENLKMLNHAPSVQIHDVPADLLTYDRTDEA.AE.RGPEENYSRPEAPNEF.D
Retrocopy IENQNSRQYLDQIRQTIFENLKMLNHAPSVQIHDVPADLLTYDRTDEANAEDRGPEENYSRPEAPNEFCD

Parental  GDHDNDKESDVEI
          GDH.NDKESDVEI
Retrocopy GDHNNDKESDVEI

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	0.00 RPM	24.65 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	23.24 RPM
SRP007412_cerebellum	0.06 RPM	30.87 RPM
SRP007412_heart	0.00 RPM	18.02 RPM
SRP007412_kidney	0.00 RPM	40.14 RPM
SRP007412_liver	0.04 RPM	12.75 RPM
SRP007412_testis	0.34 RPM	63.44 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_49 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_49 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_49 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008662	1 retrocopy	retro_mluc_642,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Macaca mulatta	ENSMMUG00000012588	1 retrocopy	retro_mmul_49 ,
Procavia capensis	ENSPCAG00000010817	1 retrocopy	retro_pcap_298,
Ictidomys tridecemlineatus	ENSSTOG00000016240	1 retrocopy	retro_itri_1661,
Tupaia belangeri	ENSTBEG00000007520	1 retrocopy	retro_tbel_1811,