RetrogeneDB ID: retro_mmul_1071

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:70348066..70348426(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: U2AF1
• Ensembl ID: ENSMMUG00000022769
• Aliases: None
• Description: None

Sequence

>retro_mmul_1071
TTTTGCAGTGAGGAAGATGTGGAAAAGGCTGTGATTGACTTGAATAACCGTTGGTTTAATGGACAGCCAATCCACGTGGA
GCTGTTGCCTGTGACCGACTTCAGAGAAGCCTGCTGCTGTCAGTATGAGATGGGAGAATGCACATGAGGCGGCTTCTGCA
ACTTCATGCATTTGAAGCCCATCTCCAGAGAGCCGTGGCAGGAGCTGTATGGGCGCCATTGCAAGAAGTGTAGATCAAGA
TCCCCATCCCTGGAGCATAGTTCTCGGTCTAGAGACCGTGGCCGTAGTGGTGGTGGAGGTGGTGGCAGAGGCCAGCATGA
CAGGAGGCCATCTAGAGATCACGAAAGATCTGGGCGATTC

Alignment

ORF - retro_mmul_1071 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.23 %
• Parental protein coverage: 51.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FRREEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRELY
          F..EED.EKAVIDLNNRWFNGQPIH.EL.PVTDFREACC.QYEMGECT.GGFCNFMHLKPISRE...ELY
Retrocopy FCSEEDVEKAVIDLNNRWFNGQPIHVELLPVTDFREACCCQYEMGECT*GGFCNFMHLKPISREPWQELY

Parental  GRRRKKHRSRSRSRERRSRSRDRGRGGGGGGGGGGGGRERDRRRSRDRERSGRF
          GR..KK.RSRS.S.E..SRSRDRGR.GGGGGG.G......DRR.SRD.ERSGRF
Retrocopy GRHCKKCRSRSPSLEHSSRSRDRGRSGGGGGGRG----QHDRRPSRDHERSGRF

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	19.61 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	25.07 RPM
SRP007412_cerebellum	0.06 RPM	31.51 RPM
SRP007412_heart	0.00 RPM	25.03 RPM
SRP007412_kidney	0.00 RPM	27.23 RPM
SRP007412_liver	0.00 RPM	21.53 RPM
SRP007412_testis	0.04 RPM	110.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1071 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1071 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1071 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_790
Pan troglodytes	retro_ptro_549
Pongo abelii	retro_pabe_703

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015558	1 retrocopy	retro_ecab_1081,
Homo sapiens	ENSG00000160201	2 retrocopies	retro_hsap_1478, retro_hsap_790,
Loxodonta africana	ENSLAFG00000011460	1 retrocopy	retro_lafr_1135,
Macaca mulatta	ENSMMUG00000014054	1 retrocopy	retro_mmul_2030,
Macaca mulatta	ENSMMUG00000022769	2 retrocopies	retro_mmul_1071 , retro_mmul_2126,
Mus musculus	ENSMUSG00000061613	3 retrocopies	retro_mmus_1602, retro_mmus_1787, retro_mmus_2955,
Nomascus leucogenys	ENSNLEG00000014737	1 retrocopy	retro_nleu_2382,
Otolemur garnettii	ENSOGAG00000016504	1 retrocopy	retro_ogar_241,
Pongo abelii	ENSPPYG00000011463	2 retrocopies	retro_pabe_1227, retro_pabe_703,