RetrogeneDB ID: retro_mmul_1726

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:138167088..138167953(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4980
• Ensembl ID: ENSMMUG00000012989
• Aliases: HNRNPA1, HNRPA1, hnRNP A1
• Description: None

Sequence

>retro_mmul_1726
CTGAGCTTTGAAACAGCCCATGAGAATCTGAGGATCCATTTTGAGCAATGGGGAATGCTCATGGGTTGTGTGGTAATGAG
AGATCCAAACACCAAACCCTGCAGGGGCTTTGGGTTTGTCACAAATGCCACTGTAGAGGAGGTGGATGCAGCCCTGAATT
AAAGGCCACACAAGGTGGAGGGAAGAGTTGTGGAAGCAAAGAGGGCCAACTCAAGAGAAGATTCTCAAAACCAGGTACCC
ACCCAACTGTGAAAAAGATATTTATAGGTGCCATTAAAGAACACACAGAAGAACATTACCTAAGAGACTATTTGGAACAG
TGTGCGATATTTAAACTGATTGCAAACATCACTGACAGAGGCAGTGGGAAGAAAAGGCTTTGGTTTTGTAAACACTGACT
ACAGTGATTCTGTGGACCAGACTGTCATTCAGAAATACCATACTGCGAATGGCCACAACTGTGAAGGAAGGAAAGCCCTG
CGAAAACAAGAGATGGGTAGTGCTTCATCCAGCCAGAGATTGGCATGGTTCTGGAAACTTTGGTGGTGGTTGTCGAAGTG
GTTTCAGTGGCAATGACAACTTTGGTCATGGAGGAAACTTCAAGGGTCATGGTGGCTTTGATGGGGATAGCTATAATGGA
TTTGATAATGATGGTAGTTATGGAGGAGGCAGTCCTAGTTACTCTGGAGGAAGACGACGCTATGGAAGTGGTGGACAGGG
TTATAGAAACCAGGGCAGTGGCTATGGTGGGAGTGGCAGCTATAACAGCTGTGTCAGTGGAAGAGGTGGAAGTGACTCTG
GTGGTGGTAGTGAAAGCAATTTTGGAAGTAGTGGAAGCTACAGTGATTTTGGAAATTACAACAAT

Alignment

ORF - retro_mmul_1726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 79.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV
          LSFET..E.LR.HFEQWG.L..CVVMRDPNTK..RGFGFVT.ATVEEVDAA.N.RPHKV.GRVVE.KRA.
Retrocopy LSFETAHENLRIHFEQWGMLMGCVVMRDPNTKPCRGFGFVTNATVEEVDAALN*RPHKVEGRVVEAKRAN

Parental  SREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS-GKKRGFAFVTFDDHDS
          SREDSQ..PG.H.TVKKIF.G.IKE.TEEH.LRDY.EQ......I...TDRGS.G.K.GF.FV..D..DS
Retrocopy SREDSQ<KPGTHPTVKKIFIGAIKEHTEEHYLRDYLEQCAIFKLIANITDRGS>GRK-GFGFVNTDYSDS

Parental  VDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQ-RGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGG
          VD..VIQKYHT.NGHNCE.RKAL.KQEM.SA.SS..R...GSGNFGGG...GF.GNDNFG.GGNF.G.GG
Retrocopy VDQTVIQKYHTANGHNCEGRKALRKQEMGSA-SSS>RDWHGSGNFGGGCRSGFSGNDNFGHGGNFKGHGG

Parental  FGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGG
          F.G......Y.G........G....Y.GG...Y..G..GY...G.GYG..GS.............GGG..
Retrocopy FDGD----SYNGFDNDGSYGGGSPSYSGGRRRYGSGGQGYRNQGSGYGGSGSYNSCVSGRGGSDSGGGSE

Parental  FGGGSGSNFGGGGSYND
          ...GS.......G.YN.
Retrocopy SNFGSSGSYSDFGNYNN

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	0.11 RPM	72.61 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	144.14 RPM
SRP007412_cerebellum	0.32 RPM	88.27 RPM
SRP007412_heart	0.00 RPM	141.68 RPM
SRP007412_kidney	0.00 RPM	70.66 RPM
SRP007412_liver	0.00 RPM	68.12 RPM
SRP007412_testis	0.04 RPM	87.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1726 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1726 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1726 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006580	16 retrocopies	retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360, retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
Dasypus novemcinctus	ENSDNOG00000009228	7 retrocopies	retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
Macaca mulatta	ENSMMUG00000012989	5 retrocopies	retro_mmul_1031, retro_mmul_1427, retro_mmul_1726 , retro_mmul_187, retro_mmul_1871,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,