RetrogeneDB ID: retro_mmul_1197

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:81192439..81193044(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000012166
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUDS3
• Ensembl ID: ENSMMUG00000020629
• Aliases: None
• Description: None

Sequence

>retro_mmul_1197
ATGAGTGCCGCGGGGCTGCTGGCCCCGGCCTCGGCCCAGGCTGAAGCGCCGCCAGCCCCCAAGTACTACCCAGAGGAGGA
CGAAGAGCTGGAGAGCGCCGAGGACGAGCTTAGCTGTCCGGGCCGCGAGTCGGACGAAGACACTGAGGATAGTGAAACTG
ACCTGGCAAAGCATGATGAAGAAGACTATGTAGAAATGAAGGAACAGATGTATCAGGACAAACTGGCTTCTCTCAAGAGG
CAGTTGCAACAACCACAAGAAGGTACATTACAGGAATATCAGAAAAGAATGAAAAAACTAGATCAGCGGTACAAAGAGAG
GATACGGAATGCAGAACTCTTCCTCCAGCTGGAAACTGAACAAGTGGAACGAAATTACGTTAAAGAAAAGAAGGCAGCAG
TGAAAGAATTTAAAGACAAGAAGGTTGAGCTGAAAGAGAACCTGATTGCTGAGCTAGAAGAAAAGAAGAAAATGGTCGAA
AACGAAAAGCTGACAATGAACTGACTGGAGATTCTATGGAGGTGAAACCTATCATGACCAGAAAGTTGCAGAGGCGAACA
AATGATTCCGTCCCCATCCCAAACAAGAGGAGGAAACCTGCTCCA

Alignment

ORF - retro_mmul_1197 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.83 %
• Parental protein coverage: 61.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSAAGLLAPAPAQAGAPPAPEYYPEEDEELESAEDDERSCRGRESDEDTEDASETDLAKHDEEDYVEMKE
          MSAAGLLAPA.AQA.APPAP.YYPEEDEELESAED.E.SC.GRESDEDTED.SETDLAKHDEEDYVEMKE
Retrocopy MSAAGLLAPASAQAEAPPAPKYYPEEDEELESAED-ELSCPGRESDEDTED-SETDLAKHDEEDYVEMKE

Parental  QMYQDKLASLKRQLQQLQEGTLQEYQKRMKKLDQQYKERIRNAALRAVLQNTEQVERNYIKEKKAAVKEF
          QMYQDKLASLKRQLQQ.QEGTLQEYQKRMKKLDQ.YKERIRNA.L...L..TEQVERNY.KEKKAAVKEF
Retrocopy QMYQDKLASLKRQLQQPQEGTLQEYQKRMKKLDQRYKERIRNAELFLQLE-TEQVERNYVKEKKAAVKEF

Parental  EDKKVELKENLIAELEEKKKMIENEKLTM-ELTGDSMEVKPIMTRKLRRRPNDPVPIPDKRRKPAP
          .DKKVELKENLIAELEEKKKM.ENEKLTM.ELTGDSMEVKPIMTRKL.RR.ND.VPIP.KRRKPAP
Retrocopy KDKKVELKENLIAELEEKKKMVENEKLTM<ELTGDSMEVKPIMTRKLQRRTNDSVPIPNKRRKPAP

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	2.02 RPM	13.45 RPM
SRP007412_brain_prefrontal_cortex	1.51 RPM	15.71 RPM
SRP007412_cerebellum	0.77 RPM	6.59 RPM
SRP007412_heart	0.59 RPM	5.89 RPM
SRP007412_kidney	2.46 RPM	9.15 RPM
SRP007412_liver	0.44 RPM	3.36 RPM
SRP007412_testis	2.53 RPM	21.79 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1197 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1197 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1197 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000001274	1 retrocopy	retro_lafr_248,
Macaca mulatta	ENSMMUG00000020629	1 retrocopy	retro_mmul_1197 ,