RetrogeneDB ID: retro_mmul_1574

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:14886093..14886988(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC17
• Ensembl ID: ENSMMUG00000013160
• Aliases: None
• Description: None

Sequence

>retro_mmul_1574
ATGGCGGTGACCAAGGAGCTCTTGCAGATGGACCTGTACGCGCTTCTAGGCATCGAGCAGACAGCAACAGACAAAGAGGT
GAAGAAGGCCTACAGGCAGAAGGCCCTCTCCTGCCACCCAGACAAAAATCCCGATAATCCCAGAGCCGCTGAACTCTTCC
CCCAGCTTTCTCGGGCCTTAGAGGTACTGACCGATGCTACAGCCAGGGTTACCTATGACAAGGTCAGGAAAGCCAGGAAG
CAGGCAGCAGAGACGACCCAGAAACTTAATGACAGAAGGAAGAGAGTGAGGCTCGAACTGGAGGCCCGGGAGCAGCAGGC
CCAGGCTCAAAGGAGCGAGGATGCTGAGGGCAGCAGGAACCCCAGGACTCTGGAGCAAGAGATACAGCGCCTGCGAGAAG
AGGGCTTCCGGCAGCTGGAGGAACAGCAGAAGCTGTTCCGGGAGCAGATCCTCCAGGCACGTGCCCAGAGGTGGAAAGAA
AAGGCCGAGAGCACCAGAGGCAGAGGAACCCCCAAACTGAAGCTCAAATGGAAGTGCAAGACGGAGGATGCGTCAAAAGG
CGGCTACTCCCAAGGTGTCCTTCTGCAGCTTTTGCAGAAGTACGGTGAGGTTCACAACCCGGTGCTTTCCAGCAAGAAAG
CAGGCGTCGCCGTGGTGGAGTTTGAGACGGTCAAGTCTGCCAAGCTGGCCGTCCGGAATGAGGTTGGCTTGGTGGAGAAC
CCTCTGAAGATTTCCTGGTTGGAGGGACGGCTCCAGGGCGCTGTGGGCCCCAGCAACCCAGGGCGGTCCAAAGACTCAGT
GCTATGAGAAAGGGACTTTGACAGCCTCGTCATGATGCGCATGCGTGCGGCAGCGGAGCGCCAACAGCTGATCACTCAGG
CTGCAGCAGCAGGAT

Alignment

ORF - retro_mmul_1574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.26 %
• Parental protein coverage: 98.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVTKELLQMDLYALLGIEEKAADKEVKKAYRQKALSCHPDKNPDNPRAAELFHQLSQALEVLTDAAARA
          MAVTKELLQMDLYALLGIE..A.DKEVKKAYRQKALSCHPDKNPDNPRAAELF.QLS.ALEVLTDA.AR.
Retrocopy MAVTKELLQMDLYALLGIEQTATDKEVKKAYRQKALSCHPDKNPDNPRAAELFPQLSRALEVLTDATARV

Parental  AYDKVRKAKKQAAERTQKLDEKRKKVKLDLEARERQAQAQESEEEEESRSTRTLEQEIERLREEGSRQLE
          .YDKVRKA.KQAAE.TQKL...RK.V.L.LEARE.QAQAQ.SE..E.SR..RTLEQEI.RLREEG.RQLE
Retrocopy TYDKVRKARKQAAETTQKLNDRRKRVRLELEAREQQAQAQRSEDAEGSRNPRTLEQEIQRLREEGFRQLE

Parental  EQQRLIREQIRQEHDHRLRGKAENTEGQGTPKLKLKWKCKKEDESKSGYSKDVLLRLLQKYGEVLNLVLS
          EQQ.L.REQI.Q....R...KAE.T.G.GTPKLKLKWKCK.ED.SK.GYS..VLL.LLQKYGEV.N.VLS
Retrocopy EQQKLFREQILQARAQRWKEKAESTRGRGTPKLKLKWKCKTEDASKGGYSQGVLLQLLQKYGEVHNPVLS

Parental  SKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEGQPQGAVGHSHSGLSKGSVLSERDYESLVMMR
          SKK.G.AVVEF.TVK.A.LAV.NEVGLV.NPLKISWLEG..QGAVG.S..G.SK.SVL.ERD..SLVMMR
Retrocopy SKKAGVAVVEFETVKSAKLAVRNEVGLVENPLKISWLEGRLQGAVGPSNPGRSKDSVL*ERDFDSLVMMR

Parental  MRQAAERQQLIA-RMQQED
          MR.AAERQQLI..R.QQ.D
Retrocopy MRAAAERQQLIT>RLQQQD

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	4.15 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.52 RPM
SRP007412_cerebellum	0.00 RPM	7.43 RPM
SRP007412_heart	0.00 RPM	4.89 RPM
SRP007412_kidney	0.00 RPM	3.29 RPM
SRP007412_liver	0.00 RPM	4.63 RPM
SRP007412_testis	0.00 RPM	4.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1574 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1574 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017, retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574 ,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,