RetrogeneDB ID: retro_mmul_1631

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:109527029..109528857(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN2L
• Ensembl ID: ENSMMUG00000003298
• Aliases: None
• Description: None

Sequence

>retro_mmul_1631
GCCTCCTCTGCAGCTCCACCGGGGCCTCCTGCGGCCTCCTCCCCCTGCCTGGGGCCTTCGGCTGCCAGGAGCGGGCTCCG
CTGGGAAGCCAAAAGCATCTTGGTAACGCAGCTGCCTCCGCAGCAGCAGCACCAGGAGAGGCCGGGGGCCGCTGCCACTG
GCAGCGCCAGGGGACAAAGCACAGGAAAGGGACCCCCACAGTCACGTGTGTTTGAAGGCGTGTACAACAATTCCAGAATG
CTGCATTTCCTTACAGCTGTTGTGGGCTCCACTTGTGATGTAAAGGTGAAAAATGACACCATCTATGAGGGTATCTTCAA
GAGGCTGAGCTCAAATTTTGAACTAGCAGTGGATGTTGTACACCAGAAAGCATCTGAGCCAGCAGGTGGTCCTTGTCGGG
AGGATATTGTAGACACCATGGTGTTTAAGCCAAGTGATGTCATGCTTGTTCACTTCTGAAATGCTGACTTCAGCTACGCT
GCTAAAGACAAGTTCACCCATTCAGCCATCGCCATTAACTAGAAGGGAATGGGGAACACAAAGAGAAGGTGCTTCAGCGC
TGGGAGGGGGGTGACAGCAACAGCGACAACTATGACCTTGAGTCCGACATGTCCAATGGATGGGACCCCAATGAAATGTT
CAAGTTCAACGAGGAGAACTACGGTGTGAAGACCACCTGTGATAGCAGTCTTTTTTCTTATACAGTGCCCTTAGAAAAGG
ACAGCTCGGAAGAGTTTCAGCAGCGAGACCTGCGTTTGGCGCAGTTGGCATGAGAGATTGAATCAAGCCCTCAGTACCGC
CTGTGGATCGCCATGGAGAGTGATGATGGGCCACTGGAGTGGAGAAGCACAGGGCGGCCCAATGGCAGTATTCAGGGCAG
GAGAGCCCCAGGTTGGCATCCAGGAAGATAAAGTATATCATCCCTCTGCCTCAATGAGTCCAGGAAGGTCCCCAGGGAGG
AGTTTGATGCAGCAGCTCTCCGTGTGGTCGGCCTGGCCTTAGCTCTTTGCCACCTCGTGGCCCTCACCATCTGGACAATA
GCAACCCTGGCCCAGGTTCTGAGGCCCGTGGTATCAATGGAGGCCCTTCCTGCATGTCCCCAAAGGCACAGAGGCCTCTG
AGAGGTGCCAAGACCCTGTCTTCACCCAATAATAGGCCTTCTGGAGAAACTTCTGTTCCTCCTCCTGCAGTGGGCCGGAT
ATATCCCCTGAGTTCTCCCAAGTCTGCTGCCCCTGCCCCAATCTCAGCTTCCTGTCTTGAGCCTCCCATTGGCTTGGCAG
TGCCAACATCTTCAGCCTCCATCCCTGTGACCTCATCAGTCTCAGATCCTGGAATGGGCTCCATTTCCTCAGTTTCTCCA
AAGATCTCCCTGGCCCCCACAGATGTAAAAGAACTCTCTACCAAGGAAACTGAGAGAACCCTGGAGCCCCAGTAGCTGGC
TCAGATAGCTGGGAAAGTCCCTGGTCTTCAGAATGAACAGAAACTATTCCAACTGGAAGAACTCAGAAAGTTTGGGGCCC
AGTTTAAGCTTCAGCCCAATAGTTCCCCTGAGAACAGCCTGGATCCTTTTCCTCCCTGGATCTTAAAGGAGGAGGCCAAA
GGAAAGGAGAAGGAGGCTGATGGTTTGTTGACTTCAGATCCCATGGGGTTCCCTCCAAGACAGAGTCCATATGGGATAAG
GAAGACAGACCACCCCTGGCACCAGCAGGAGGCACTGAGGGTCCAGAACAGAGCCTCCCCCCCACCTTGCCCAAGCCAAA
CCAGCAGCCCCCCAGTTGGGCTCATCAAAGGAGAGGACAAGGATGAGGGCCCTATTGCTGAACAAGTA

Alignment

ORF - retro_mmul_1631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.36 %
• Parental protein coverage: 58.93 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ATSAAPPGPPAAASPCLGPVATTGSGLRRGAEGILAPQPPPPPPQQHQERPGAAAIGSARGQSTGKGPPQ
          A.SAAPPGPPAA.SPCLGP.A...SGLR..A..IL..Q.PP...QQHQERPGAAA.GSARGQSTGKGPPQ
Retrocopy ASSAAPPGPPAASSPCLGPSAAR-SGLRWEAKSILVTQLPPQ--QQHQERPGAAATGSARGQSTGKGPPQ

Parental  SPVFEGVYNNSRMLHFLTAVVGSTCDVKVKNGTTYEGIFKTLSSKFELAVDAVHRKASEPAGGPRREDIV
          S.VFEGVYNNSRMLHFLTAVVGSTCDVKVKN.T.YEGIFK.LSS.FELAVD.VH.KASEPAGGP.REDIV
Retrocopy SRVFEGVYNNSRMLHFLTAVVGSTCDVKVKNDTIYEGIFKRLSSNFELAVDVVHQKASEPAGGPCREDIV

Parental  DTMVFKPSDVMLVHFRNVDFNYATKDKFTDSAIAMNSKV-NGEHKEKVLQRWEGGDSNSDDYDLESDMSN
          DTMVFKPSDVMLVHF.N.DF.YA.KDKFT.SAIA.N.K..NGEHKEKVLQRWEGGDSNSD.YDLESDMSN
Retrocopy DTMVFKPSDVMLVHF*NADFSYAAKDKFTHSAIAIN*KG<NGEHKEKVLQRWEGGDSNSDNYDLESDMSN

Parental  GWDPNEMFKFNEENYGVKTTYDSSLSSYTVPLEKDNSEEFRQRELRAAQLAREIESSPQYRLRIAMENDD
          GWDPNEMFKFNEENYGVKTT.DSSL.SYTVPLEKD.SEEF.QR.LR.AQLA.EIESSPQYRL.IAME.DD
Retrocopy GWDPNEMFKFNEENYGVKTTCDSSLFSYTVPLEKDSSEEFQQRDLRLAQLA*EIESSPQYRLWIAMESDD

Parental  GRTE-EEKHSAVQRQGSGRESPSLASREGKYI-PLPQRVREGPRGGVRCSSSRGGRPGLSSLPPRGPHHL
          G..E..EKH.A.Q.Q.SG.ESP.LASR..KYI.PLPQ.V.EGP.GGV.CSSS..GRPGLSSLPPRGPHHL
Retrocopy GPLE<VEKHRAAQWQYSGQESPRLASRKIKYIIPLPQ*VQEGPQGGV*CSSSPCGRPGLSSLPPRGPHHL

Parental  DNSSPGPGSEARGINGGPSRMSPKAQRPLRGAKTLSSPSNRPSGETSVPPPPAVGRIYPPRSPKSAAPAP
          DNS.PGPGSEARGINGGPS.MSPKAQRPLRGAKTLSSP.NRPSGETSVPPP.AVGRIYP..SPKSAAPAP
Retrocopy DNSNPGPGSEARGINGGPSCMSPKAQRPLRGAKTLSSPNNRPSGETSVPPP-AVGRIYPLSSPKSAAPAP

Parental  ISASCPEPPIGSAVPTSSASIPVTSSVSDPGVGSISPASPKISLAPTDVKELSTKEPGRTLEPQELARIA
          ISASC.EPPIG.AVPTSSASIPVTSSVSDPG.GSIS..SPKISLAPTDVKELSTKE..RTLEPQ.LA.IA
Retrocopy ISASCLEPPIGLAVPTSSASIPVTSSVSDPGMGSISSVSPKISLAPTDVKELSTKETERTLEPQ*LAQIA

Parental  GKVPGLQNEQKRFQLEELRKFGAQFKLQPSSSPENSLDPFPPRILKEEPKGKEKEVDGLLTSEPMGSPVS
          GKVPGLQNEQK.FQLEELRKFGAQFKLQP.SSPENSLDPFPP.ILKEE.KGKEKE.DGLLTS.PMG.P..
Retrocopy GKVPGLQNEQKLFQLEELRKFGAQFKLQPNSSPENSLDPFPPWILKEEAKGKEKEADGLLTSDPMGFPPR

Parental  SKTESVSDKEDKPPLAPAGGTEGPEQPPPPCPSQTGSPPVGLIKGEDKDEGPVAEQV
          .................A........PP.PCPSQT.SPPVGLIKGEDKDEGP.AEQV
Retrocopy QSPYGIRKTDHPWHQQEALRVQNRASPP-PCPSQTSSPPVGLIKGEDKDEGPIAEQV

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	96.36 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	120.90 RPM
SRP007412_cerebellum	0.00 RPM	121.66 RPM
SRP007412_heart	0.00 RPM	43.34 RPM
SRP007412_kidney	0.00 RPM	58.57 RPM
SRP007412_liver	0.00 RPM	62.54 RPM
SRP007412_testis	0.38 RPM	1222.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1631 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1631 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1631 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3820
Pan troglodytes	retro_ptro_2598
Gorilla gorilla	retro_ggor_2570

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000168488	1 retrocopy	retro_hsap_3820,
Gorilla gorilla	ENSGGOG00000014112	1 retrocopy	retro_ggor_2570,
Macaca mulatta	ENSMMUG00000003298	1 retrocopy	retro_mmul_1631 ,
Pan troglodytes	ENSPTRG00000007938	1 retrocopy	retro_ptro_2598,