RetrogeneDB ID: retro_mmul_534

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:132954308..132954652(-)
• Located in intron of: ENSMMUG00000022978

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSMMUG00000031219
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_mmul_534
AAGCTAGTTCTTCTGGAGCTCAAATTCTTGCCAACCACAGGGACCAAGCTGACCAAACAGCAGCTCATTCTAGCCCGTGA
CATACTGGAGATCGGGGCCAGTGGAGCATCCTATGCAAGGACATCCCCTCCTTCAAGCGCCACATGGCCCAGCCCAAATG
GTGCTACTTTGATTACAAGGAACAGCTTCCCGAGTCAGCCTACATGCACCAGCTCTTGGGCCTCAACCTCCTCTTCCTGC
TGTCCCAGAAGCAGGTGGCTGAGTTCCACATGGAGTTGGAGCGGCTGCCTGCCAAGGACATCCAGACCAATGTCTACATC
AAACACCCTGTGCCACTGGAGCAA

Alignment

ORF - retro_mmul_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.79 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QLVLLELNFLPTTGTKLTKQQLILARDILEIGA-QWSILRKDIPSFERYMAQLKCYYFDYKEQLPESAYM
          .LVLLEL.FLPTTGTKLTKQQLILARDILEIGA.QWSIL.KDIPSF.R.MAQ.K..YFDYKEQLPESAYM
Retrocopy KLVLLELKFLPTTGTKLTKQQLILARDILEIGA<QWSILCKDIPSFKRHMAQPKWCYFDYKEQLPESAYM

Parental  HQLLGLNLLFLLSQNRVAEFHTELERLPAKDIQTNVYIKHPVSLEQ
          HQLLGLNLLFLLSQ..VAEFH.ELERLPAKDIQTNVYIKHPV.LEQ
Retrocopy HQLLGLNLLFLLSQKQVAEFHMELERLPAKDIQTNVYIKHPVPLEQ

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	1.34 RPM	10.98 RPM
SRP007412_brain_prefrontal_cortex	10.15 RPM	31.02 RPM
SRP007412_cerebellum	2.13 RPM	9.62 RPM
SRP007412_heart	1.71 RPM	8.36 RPM
SRP007412_kidney	2.00 RPM	11.62 RPM
SRP007412_liver	6.89 RPM	20.58 RPM
SRP007412_testis	6.03 RPM	31.62 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_534 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_534 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000006596	2 retrocopies	retro_meug_1494, retro_meug_173,
Macaca mulatta	ENSMMUG00000031219	1 retrocopy	retro_mmul_534 ,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,