RetrogeneDB ID: retro_mmul_936

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:10947133..10948062(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000023092
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.193
• Ensembl ID: ENSMMUG00000008872
• Aliases: None
• Description: alpha-internexin [Source:RefSeq peptide;Acc:NP_001253499]

Sequence

>retro_mmul_936
GGACGCTAAGGCGCCGAGGGTGCCCTGAAGGCGCAGTAGCGCGACATGGACTGCGCCACGCTGGCCCGCCTGGACCTGGA
AAAGAAGCTGGAGTCGCTGCTGGACGAGCTGGCCTTCGTGCGCCAGGTGCACGACGAGGAGGTAGCTGAGCTACTGGCCA
CGCTTCAGGCGTCGTCGCAGGCCGCGGCCGAGGTGGATGGGGCTGTGGCTAAACCAGATCTGACCTCGGCGCTGAGGGAG
ATCCGCGCCCAGTATGAGTCCCTGGCCGCTAAGAACCTGCAGTCCGCGGAAGAATGGTACAAGTCCAAGTTCGCCAACCT
GAACGCGCAGGCGGCGCGCAGCATAGAGGCCATCCGGACCAGCGGCGAGGAGATCCATGAATACCGGCGCCAGCTGCAGG
CGCGCACCAGCGAGATCGAGGGCCTGCGCGGGGCCAACGAGTCCTTGGAGAGGCAGATCCTGGAGCTGGAGGAGCGGCAC
GGTGCCGAGGTGGCTGGTTACCAGGGTAGCATTGGGCAGCTGGAGAATGATCTGAGGAACACCAAGAGTGATATGGCACT
CCACATTCGGGAATACCAGGACTTGCTCAATGTCAAAATGGCTCTTGACATTGAGATAGCAGCTTACAGGAAACTGCTGG
AAGGTGAGGAGACACGTTTTAGCACCAGTGGGTTAGGCATTTCGAGGCTGAATCCACTTTCCAATCCAAGTTATCCGCTC
CCACCTAGAATCCTCAGTTCTACAACCTCCAAGTCTCATCCACTGGGCTATCACTTAAGAAAGAGGAGGAGGAGGCATCT
GAGGTAGCTTCTAAGAAAACTTCCCAGATAGAGGAAAGTTTTGAAGAAATATTAGAGGAGACAGTGATATCTACTAAGAA
AACCAAGAAATCAAATATAGAAGAAACCACCCTTTCAAGCCAAAAAATA

Alignment

ORF - retro_mmul_936 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.73 %
• Parental protein coverage: 62.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GREGAERALKAQQRDVDGATLARLDLEKKVESLLDELAFVRQVHDEEVAELLATLQASSQAAAEVDVAVA
          GR.GAE.ALKAQ.RD.D.ATLARLDLEKK.ESLLDELAFVRQVHDEEVAELLATLQASSQAAAEVD.AVA
Retrocopy GR*GAEGALKAQ*RDMDCATLARLDLEKKLESLLDELAFVRQVHDEEVAELLATLQASSQAAAEVDGAVA

Parental  KPDLTSALREIRAQYESLAAKNLQSAEEWYKSKFANLNEQAARSTEAIRASREEIHEYRRQLQARTIEIE
          KPDLTSALREIRAQYESLAAKNLQSAEEWYKSKFANLN.QAARS.EAIR.S.EEIHEYRRQLQART.EIE
Retrocopy KPDLTSALREIRAQYESLAAKNLQSAEEWYKSKFANLNAQAARSIEAIRTSGEEIHEYRRQLQARTSEIE

Parental  GLRGANESLERQILELEERHSAEVAGYQDSIGQLENDLRNTKSEMARHLREYQDLLNVKMALDIEIAAYR
          GLRGANESLERQILELEERH.AEVAGYQ.SIGQLENDLRNTKS.MA.H.REYQDLLNVKMALDIEIAAYR
Retrocopy GLRGANESLERQILELEERHGAEVAGYQGSIGQLENDLRNTKSDMALHIREYQDLLNVKMALDIEIAAYR

Parental  KLLEGEETRFSTSGLSISGLNPLPNPSYLLPPRILSSATSK-VSSTGLSLKKEEEEEEASKVASKKTSQI
          KLLEGEETRFSTSGL.IS.LNPL.NPSY.LPPRILSS.TSK.VSSTGLSLKK..EEEEAS.VASKKTSQI
Retrocopy KLLEGEETRFSTSGLGISRLNPLSNPSYPLPPRILSSTTSK<VSSTGLSLKK--EEEEASEVASKKTSQI

Parental  GESFEEILEETVISTKKTEKSNIEETTISSQKI
          .ESFEEILEETVISTKKT.KSNIEETT.SSQKI
Retrocopy EESFEEILEETVISTKKTKKSNIEETTLSSQKI

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	0.22 RPM	267.46 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	209.91 RPM
SRP007412_cerebellum	0.00 RPM	219.17 RPM
SRP007412_heart	0.00 RPM	0.35 RPM
SRP007412_kidney	0.00 RPM	0.23 RPM
SRP007412_liver	0.00 RPM	0.04 RPM
SRP007412_testis	0.57 RPM	4.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_936 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_936 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_936 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018178	4 retrocopies	retro_cjac_1685, retro_cjac_394, retro_cjac_4043, retro_cjac_760,
Macaca mulatta	ENSMMUG00000008872	1 retrocopy	retro_mmul_936 ,
Nomascus leucogenys	ENSNLEG00000015236	1 retrocopy	retro_nleu_795,