RetrogeneDB ID: retro_mmul_187

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:54484537..54485365(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000011937
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_mmul_187
GTAGTGGAACCAAAGAGAGCTGTTTCTAGAGAGGATTCTGTAAAGCCTGGTGCCCATCTAACAGTGAAGAAAATTTTTGT
TGGTGGTATTAAAGAAGATACAGAAGAATATAATTTGAGAGACTACTTTGAAAAGTATGGCAAAATTGAAACCATAGAAG
TTATGGAAGACAGGCAGAGTGGAAAAAAGAGAGGATTTGCTTTTGTAACTTTTGATGATCATGATACAGTTGATAAAATT
GTTGTTCAGAAATACCACACTATTAATGGGCATAATTGTGAAGTGAAAAAGGCCCTTTCTAAACAAGAGATGCAGTCTGC
TGGATCACAGAGAGGTCGTGGAGGTGGATCTGGCAATTTTATGGGTCGTGGAGGAAACTTTGGAGGTGGTGGAGGTAATT
TTGGCCGTGGTGGAAACCTTGGTGGAAGAGGAGGCTATGGTGGTGGAGGTGGTGGTAGCAGAGGTAGTTATGGTGGAGGT
GATGGTGGATATAATGGATTTGGAGGTGATGGTGGCAACTATGGCGGTGGTCCTGGTTATAGTAGTAGAGGGGGCTATGG
TGGTGGTGGACCAGGATATGGAAACCAAGGTGGTGGATATGGTGGCAGTGGTGGAGGATATGATGGTTACAATGAAGGAG
GAAATTTTGGCGGTAACTATGGTGGTGGTGGGAACTATAATGATTTTGGAAATTATAGTGGACAACAGCAGTCAAATTAT
GGACCCATGAAAGGGGGCAGTTTTGGTGGAAGAAGCTCGGGCAGTCCCTATGGTGGTGGTTATGGATCTGGTGGTGGAAG
TGGTGGATATGGTAGCAGAAGGTTCTAA

Alignment

ORF - retro_mmul_187 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.04 %
• Parental protein coverage: 70.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT
          VVEPKRAVSREDS..PGAHLTVKKIFVGGIKEDTEE..LRDYFE.YGKIE.IE.M.DR.SGKKRGFAFVT
Retrocopy VVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVT

Parental  FDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGF-GGNDNFGRGGN
          FDDHD.VDKIV.QKYHT.NGHNCEV.KALSKQEM.SA.S......GSGNF..GRGG.F.GG..NFGRGGN
Retrocopy FDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNF-MGRGGNFGGGGGNFGRGGN

Parental  FSGRGGFGGSRGG--GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGS-GSYD
          ..GRGG.GG..GG..G.YGG...GYNGFG.DGG..GGGPGYS....GYG.GG.GYGNQG.GYGGS.G.YD
Retrocopy LGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRG-GYGGGGPGYGNQGGGYGGSGGGYD

Parental  SYNNGGGGGFGGGSGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGG
          .YN.GG..G...G.G.N....G.Y......N......G...G...G....G.YG.GG
Retrocopy GYNEGGNFGGNYGGGGNYNDFGNYSGQQQSNYGPMKGGSFGGRSSGSPYGGGYGSGG

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	14.12 RPM	72.61 RPM
SRP007412_brain_prefrontal_cortex	15.87 RPM	144.14 RPM
SRP007412_cerebellum	16.79 RPM	88.27 RPM
SRP007412_heart	24.26 RPM	141.68 RPM
SRP007412_kidney	14.79 RPM	70.66 RPM
SRP007412_liver	18.68 RPM	68.12 RPM
SRP007412_testis	77.65 RPM	87.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_187 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_187 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,