RetrogeneDB ID: retro_mmul_915

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:46929156..46930542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC3
• Ensembl ID: ENSMMUG00000006350
• Aliases: None
• Description: None

Sequence

>retro_mmul_915
GACCTCCTGCCCCCCGAAGTCTGCAGTCTCCTGAACCCAGCAGCCATCTATGCCAACAAGGAGATCAGCCTGCGTGACGT
TGAGGTCTATGGCTTTGACTACGACTACACTCTGGCCCAGTATGCAGATGCACTGCACCCCGAGATCTTCGGCGCCGCCC
GTGACATCCTGATCGAGCACTACAAGTACCCAGGGGGGATTCGGAAGTATGACTACAACCCCAGCTTTGCCATCCGTGGC
CTCCACTATGACATTCAGAAGAGCCTTCTGATAAAGATTGACGCCTTCCACTACGTGCAGCTGGGGACAGCCTACAGGGG
CCTCCAGCCTGTGCCAGATGAGGAAGTGATCGAGCTGTATGGGGGCACCCAGCACATCCCACTATACCAGATGAGTGGCT
TCTATGGCAAGGGTCCCTCCATTAAGCAGTTCATGGACATCTTCTCGCTGCCGGAGATGGCTCTGCTGTCCTGCGTGGTG
GACTACTTCCTGGGCCACAGCCTGGAGTTTGACCAAGCGCACCTCTACAAGGATGTGACAGACGCCATCCTAGAAGTGCA
TGTGAAGGTCCTCATGTACCAGTGGATCGAGCAGGACATGGAGAAGTACATCCTGAGAGGGGACGAGACGTTTGCCGTCC
TGAGTTGCCTGGTGGCCCATGGGAAACAGCTGTTCCTCATCACCAACAGTCCTTTCAGCTTCCTAGACTAAGGGATGCGG
CACACGGTGGGTCCCGATTGGCGCCAGCTCTTCGATGTGGTCATTGTCCAGGCAGACAAGCCCAGCTTTTTCACTGATCG
GCGCAAGCCTTTCAGAAAACTCGATGAGAAGGGCTCGCTTCAGTGGGACCGGATCACCCGCTTGGAAAAGGGCAAGATCT
ATCGGCAGGGAAACCTGTTTGACTTCCTTCGCTTGACGGAATGGCGTGGCCCCCGCGTGCTCTACTTCGGGGACCACCTC
TATAGTGACCTGGTGGATCTCATGCTGCGGCAGGGCTGGCGCAGGGGCGCCTTCATCCCTGAGCTGGAGCGTGAGATCCG
CATCATCAACACAGAGCAGTACATGCACTGGCTGACGTGGCAGCAAGCACTCAGGGGGCTGCTGGAGCGCATGCAGACCT
ATCAGGACGCGGAGTCCAGGCAGGTGCTAGCTGCCCGGATGAAAGAAGGGCAGGAGCTGAGGTGCGTCACCAAGGCCATG
TTCAGCGCGCAGTTTGGCAGCATCTTCCGCACCTTCCACAACCCCACCTACTTCTTGAGATGCCTCGTGCACTTCTCTGA
CCTCTACATGGCCTCCCTCAGCTGCCTGCTCAACTACCGTGTGGACTTCACCGTCTACCTGCGCCCCACCCCGCTGCAGC
AGGAGGCGCCCCTCTGGATGGACCAG

Alignment

ORF - retro_mmul_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.37 %
• Parental protein coverage: 96.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELVPSIMSNLLNPDAIFSNNEMSLSDIEIYGFDYDYTLVFYSKHLHTLIFNAARDLLINEHRYPAEIRKY
          .L.P.....LLNP.AI..N.E.SL.D.E.YGFDYDYTL..Y...LH..IF.AARD.LI....YP..IRKY
Retrocopy DLLPPEVCSLLNPAAIYANKEISLRDVEVYGFDYDYTLAQYADALHPEIFGAARDILIEHYKYPGGIRKY

Parental  EYDPNFAIRGLHYDVQRAVLMKIDAFHYIQLGTVYRGLSVVPDEEVIEMYEGS-HVPLEQMSDFYGKSSH
          .Y.P.FAIRGLHYD.Q...L.KIDAFHY.QLGT.YRGL..VPDEEVIE.Y.G..H.PL.QMS.FYGK...
Retrocopy DYNPSFAIRGLHYDIQKSLLIKIDAFHYVQLGTAYRGLQPVPDEEVIELYGGTQHIPLYQMSGFYGK---

Parental  GNTMKQFMDIFSLPEMTLLSCVNEYFLKNNIDYEPVHLYKDVKDSIRDVHIKGIMYRAIEADIEKYICYA
          G...KQFMDIFSLPEM.LLSCV..YFL.........HLYKDV.D.I..VH.K..MY..IE.D.EKYI...
Retrocopy GPSIKQFMDIFSLPEMALLSCVVDYFLGHSLEFDQAHLYKDVTDAILEVHVKVLMYQWIEQDMEKYILRG

Parental  EQTRAVLAKLADHGKKMFLITNSPSSFVDKGMSYIVGKDWRDLFDVVIVQAEKPNFFNDKRRPFRKMNEK
          ..T.AVL..L..HGK..FLITNSP.SF.D.GM...VG.DWR.LFDVVIVQA.KP.FF.D.R.PFRK..EK
Retrocopy DETFAVLSCLVAHGKQLFLITNSPFSFLD*GMRHTVGPDWRQLFDVVIVQADKPSFFTDRRKPFRKLDEK

Parental  GVLLWDKIHKLQKGQIYKQGNLYEFLKLTGWRGSRVLYFGDHIYSDLADLTLKHGWRTGAIIPELRSELK
          G.L.WD.I..L.KG.IY.QGNL..FL.LT.WRG.RVLYFGDH.YSDL.DL.L..GWR.GA.IPEL..E..
Retrocopy GSLQWDRITRLEKGKIYRQGNLFDFLRLTEWRGPRVLYFGDHLYSDLVDLMLRQGWRRGAFIPELEREIR

Parental  IMNTEQYIQTMTWLQTLTGLLEQMQVHRDAESQLVLQEWKKERKEMREMTKSFFNAQFGSLFRTDQNPTY
          I.NTEQY....TW.Q.L.GLLE.MQ...DAES..VL....KE..E.R..TK..F.AQFGS.FRT..NPTY
Retrocopy IINTEQYMHWLTWQQALRGLLERMQTYQDAESRQVLAARMKEGQELRCVTKAMFSAQFGSIFRTFHNPTY

Parental  FLRRLSRFADIYMASLSCLLNYDVSHTFYPRRTPLQHELPAWSER
          FLR.L..F.D.YMASLSCLLNY.V..T.Y.R.TPLQ.E.P.W...
Retrocopy FLRCLVHFSDLYMASLSCLLNYRVDFTVYLRPTPLQQEAPLWMDQ

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	0.56 RPM	21.07 RPM
SRP007412_brain_prefrontal_cortex	2.22 RPM	16.02 RPM
SRP007412_cerebellum	1.68 RPM	14.14 RPM
SRP007412_heart	1.41 RPM	1.18 RPM
SRP007412_kidney	4.58 RPM	3.99 RPM
SRP007412_liver	0.20 RPM	6.02 RPM
SRP007412_testis	1.06 RPM	3.51 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_915 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_915 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_915 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
Macaca mulatta	ENSMMUG00000006350	1 retrocopy	retro_mmul_915 ,
Tursiops truncatus	ENSTTRG00000009239	1 retrocopy	retro_ttru_1040,