RetrogeneDB ID: retro_mmul_1274

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:840367..840574(+)
• Located in intron of: ENSMMUG00000013370

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMSB4X
• Ensembl ID: ENSMMUG00000014256
• Aliases: None
• Description: thymosin beta-4 [Source:RefSeq peptide;Acc:NP_001247486]

Sequence

>retro_mmul_1274
AACTCGGTGGTGGCCACTGCACAGACCAGACTTCGCTCGTTCTTGCGTGCCTCGCTCTGCTTTTCCTCCGCAACCATGTC
TGACAAACCCAATATGGCTGAGATCGAGAAATTCGATAAATCGAGACTGAAGAAGACGAGACTGCAAGAGAAAAATCCAC
CGCCTTCCAAAGAAGCGATTGAACAGGAGAAGCAAGGAGGCGAATCG

Alignment

ORF - retro_mmul_1274 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NSVVATAQTRLRSFSCASLRFSSATMSDKPDMAEIEKFDKSKLKKTETQEKNPLPSKETIEQEKQAGES
          NSVVATAQTRLRSF..ASL.FSSATMSDKP.MAEIEKFDKS.LKKT..QEKNP.PSKE.IEQEKQ.GES
Retrocopy NSVVATAQTRLRSFLRASLCFSSATMSDKPNMAEIEKFDKSRLKKTRLQEKNPPPSKEAIEQEKQGGES

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	285.39 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	489.94 RPM
SRP007412_cerebellum	0.00 RPM	126.50 RPM
SRP007412_heart	0.35 RPM	382.28 RPM
SRP007412_kidney	0.23 RPM	145.65 RPM
SRP007412_liver	0.04 RPM	110.99 RPM
SRP007412_testis	0.04 RPM	27.25 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1274 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1274 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1274 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038488	2 retrocopies	retro_btau_1731, retro_btau_599,
Gorilla gorilla	ENSGGOG00000006450	1 retrocopy	retro_ggor_200,
Macaca mulatta	ENSMMUG00000014256	2 retrocopies	retro_mmul_1274 , retro_mmul_1890,
Pan troglodytes	ENSPTRG00000028317	4 retrocopies	retro_ptro_1440, retro_ptro_1572, retro_ptro_2864, retro_ptro_77,