RetrogeneDB ID: retro_mmul_1238

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:57440613..57441410(+)
• Located in intron of: ENSMMUG00000010588

Retrocopy information

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

Parental gene information

• Parental gene symbol: UAP1
• Ensembl ID: ENSMMUG00000019514
• Aliases: None
• Description: UDP-N-acetylhexosamine pyrophosphorylase [Source:RefSeq peptide;Acc:NP_001253838]

Sequence

>retro_mmul_1238
TTCCATATAATGATCAGTGGCAGAACAGCGGAATCTACAAGGAGTTCTTCACCAAGCACAAGTACTTTGGTTTAAAAAGA
AAAGAAAATATAATCTTTTTTTCAGCAAGGAATGCTCCCTGCCATGAGTTTTGATGGGCAAATTATTTTGGAAGAGAAGA
ACAAAGTTTCTATTGCTCCACATGAGAATGGTGGTCTTTATTGGGCTCTTGCAGCCTGGCATATTGTGGAGGATATGGTG
CAAAGAGGCATTTGGAGCATTCATGTCTATTGTGTTGACAACATATTAGTAAAAGTGGCAGGCCCACGGTTCATTGGATT
TTGCATTCAGAAAGGAGCAGACTGTGGAGCAAAGGTGGTAGAGAAAACAAACCCTGCAGAACCAGTTGGAGTGGTTTGCC
GAGTGGATGGAGTTTACCAGGTGGTAGAATATAGTGATGTTTCCCTGGCAACAGCTCAAAAACGAAGCTCAAATGGATGA
TTGCCGTTCAATGTGGAGAATATTGCCAACCATTTATTCACCGTACCATTTCTGAGGATGTTGTCAATGTTTATGAACCT
CAGTTGCAGCACCATGTGGCTCAAAAGAAGATTCCTTATGTGGATACCCAACAGCACTTAATTAAGCCAGATAAGCCCAG
TGGAATCAGTATGGAAAAATTTGTCTTTGACATCTTCTAGTTTGCAAAGAAGTTTGTGGTTTATGAAATATTATGGGAAG
ATGACTTTTCCACACTAAAGAATGCTGACAGTCAGAATGGGAAAGACAATTTTACTACCGCAAGGCACACTTTCATT

Alignment

ORF - retro_mmul_1238 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.13 %
• Parental protein coverage: 52.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WYIMTSGRTMEST-KEFFTKHKYFGLK-KENVIFF-QQGMLPAMSFDGKIILEEKNKVSMAPDGNGGLYR
          ..IM.SGRT.EST.KEFFTKHKYFGLK.KEN.IFF.QQGMLPAMSFDG.IILEEKNKVS.AP..NGGLY.
Retrocopy FHIMISGRTAEST<KEFFTKHKYFGLKRKENIIFF>QQGMLPAMSFDGQIILEEKNKVSIAPHENGGLYW

Parental  ALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGV
          ALAA..IVEDM.QRGIWSIHVYCVDNILVKVA.PRFIGFCIQKGADCGAKVVEKTNP.EPVGVVCRVDGV
Retrocopy ALAAWHIVEDMVQRGIWSIHVYCVDNILVKVAGPRFIGFCIQKGADCGAKVVEKTNPAEPVGVVCRVDGV

Parental  YQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLR-DVVNVYEPQLQHHVAQKKIPYVDTQGHL
          YQVVEYS..SLATAQKRSS.G.L.FN..NIANH.FTVPFLR.DVVNVYEPQLQHHVAQKKIPYVDTQ.HL
Retrocopy YQVVEYSDVSLATAQKRSSNG*LPFNVENIANHLFTVPFLR<DVVNVYEPQLQHHVAQKKIPYVDTQQHL

Parental  VKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTARHALM
          .KPDKP.GI.MEKFVFDIF.FAKKFVVYE.L.ED.FS.LKNADSQNGKDN.TTARH...
Retrocopy IKPDKPSGISMEKFVFDIF*FAKKFVVYEILWEDDFSTLKNADSQNGKDNFTTARHTFI

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	26.67 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.88 RPM
SRP007412_cerebellum	0.00 RPM	35.19 RPM
SRP007412_heart	0.00 RPM	31.86 RPM
SRP007412_kidney	0.00 RPM	17.96 RPM
SRP007412_liver	0.04 RPM	27.59 RPM
SRP007412_testis	0.26 RPM	233.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1238 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1238 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004264	1 retrocopy	retro_cjac_2537,
Cavia porcellus	ENSCPOG00000004568	5 retrocopies	retro_cpor_1186, retro_cpor_1187, retro_cpor_1188, retro_cpor_1189, retro_cpor_511,
Dasypus novemcinctus	ENSDNOG00000024661	1 retrocopy	retro_dnov_1035,
Macaca mulatta	ENSMMUG00000019514	1 retrocopy	retro_mmul_1238 ,
Tarsius syrichta	ENSTSYG00000002725	3 retrocopies	retro_tsyr_121, retro_tsyr_390, retro_tsyr_582,