RetrogeneDB ID: retro_mmul_217

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:110302506..110303133(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000010744
• Aliases: DTD1, HARS2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DTD1
• Ensembl ID: ENSMMUG00000012880
• Aliases: None
• Description: D-tyrosyl-tRNA(Tyr) deacylase 1 [Source:RefSeq peptide;Acc:NP_001253587]

Sequence

>retro_mmul_217
ATGAAGGCCGTGTTGCAGCGCGTCACCCGGGCCAGCGTCACAGTTGGAGGAGAGCAGATTAGTGCTATTGGAAGGGGCAT
ATGTGTGTTGCTGAGTATTTCCCTGGAGGATACGCAGAAGAAACTGGAGCACATGGTCCGAAAGATTCTAAACCTGCGTG
TGTTTGACGATGACAGCGGGAAGCACTGGTCTAAGAGTGTGATGGACAAACAGTACGAGATTCTGTGTGTCAGCCAGTTT
ACCCTCCAGTGTGTCCTGAAGGGAAACAAGCCTGATTTCTACCTAGCAATGCCCACGGAGCAGGCAGAGGGCTTTTACAA
CAGCTTCCTGGAGCAGCTGCCTAAAACATACAGGCCGGGGCTTATCAAAGATGGCACGTTTGGGGCCTACATGCAGGTGT
ACATTCAGAATGATGGGCCTGTGACCACAGAGCTGGAATCGCCAGCTCCCGGCACTGCTACCTCTGATCCAAAGCAGCTG
TCAAAGCCTGAAAAACAGCAGCAGAGAAAAGAAAAGACCAGAGCTAAGGGACCTTCTGAAACAACCAAGGAAAGAAACAC
TCCCCGAAAAGAAGACCGCAGTGCCAGCAGCGGGGCCGAGGGTGACGTGTCCTCTGAATGGGAACTG

Alignment

ORF - retro_mmul_217 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 99.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKAVVQRVTRASVTVGGEQISAIGRGICVLLGISLEDTQKELEHMVRKILNLRVFEDESGKHWSKSVMDK
          MKAV.QRVTRASVTVGGEQISAIGRGICVLL.ISLEDTQK.LEHMVRKILNLRVF.D.SGKHWSKSVMDK
Retrocopy MKAVLQRVTRASVTVGGEQISAIGRGICVLLSISLEDTQKKLEHMVRKILNLRVFDDDSGKHWSKSVMDK

Parental  QYEILCVSQFTLQCVLKGNKPDFHLAMPTDQAEGFYNSFLEQLRKTYRPELIKDGKFGAYMQVHIQNDGP
          QYEILCVSQFTLQCVLKGNKPDF.LAMPT.QAEGFYNSFLEQL.KTYRP.LIKDG.FGAYMQV.IQNDGP
Retrocopy QYEILCVSQFTLQCVLKGNKPDFYLAMPTEQAEGFYNSFLEQLPKTYRPGLIKDGTFGAYMQVYIQNDGP

Parental  VTIELESPAPGTATSDPKQLSKLEKQQQRKEKTRAKGPSESSKERNTPRKEDRSASSGAEGDVSSERE
          VT.ELESPAPGTATSDPKQLSK.EKQQQRKEKTRAKGPSE..KERNTPRKEDRSASSGAEGDVSSE.E
Retrocopy VTTELESPAPGTATSDPKQLSKPEKQQQRKEKTRAKGPSETTKERNTPRKEDRSASSGAEGDVSSEWE

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	23.42 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	31.73 RPM
SRP007412_cerebellum	0.00 RPM	11.75 RPM
SRP007412_heart	0.00 RPM	6.65 RPM
SRP007412_kidney	0.00 RPM	12.56 RPM
SRP007412_liver	0.00 RPM	3.40 RPM
SRP007412_testis	0.04 RPM	32.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_217 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_217 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008964	1 retrocopy	retro_btau_767,
Macropus eugenii	ENSMEUG00000009170	2 retrocopies	retro_meug_137, retro_meug_1809,
Macaca mulatta	ENSMMUG00000012880	1 retrocopy	retro_mmul_217 ,
Monodelphis domestica	ENSMODG00000005696	1 retrocopy	retro_mdom_509,
Mus musculus	ENSMUSG00000027430	1 retrocopy	retro_mmus_2774,
Oryctolagus cuniculus	ENSOCUG00000010988	1 retrocopy	retro_ocun_1357,
Tupaia belangeri	ENSTBEG00000000242	1 retrocopy	retro_tbel_3434,