RetrogeneDB ID: retro_mmul_1427

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:42317517..42318200(+)
• 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_1427
GGCAAAAGGAGGGGCTTTTGTTTTTATAACCATGGCTCCGTAGATAAGATTGTCATTCAGAAATACCATACTGGGAATGG
CCACCACTGTGAAGTAAAGAAAGCCCTGTAGTAGCAAGAGATGGCCAGTTTTTCATCTAGCCAACGAGGCTGCAGTGGTT
CTGGAAACTTTGGTGGTGGTTGTGGAGGTGGTTTTGGTGGGAATGACAACTTTGGTCACAGAGGAAACTTCAGTGCTTGT
GGTGCCTTTGGTGGCAGCTGTGGTGATGGTGGATATGGCGGCAATTAGGATGGCTATAATGGATTTGGTAATGATAGTGG
TTATGAAGGAGGCAGCCCTGGTTACTCTGGAGGAAGCAGAGGCTATGGAAGTAGTGGACAGGATTCTGGAAACCAGGGCA
GTGGCTATGGTGGGGGTGGCAGCCGTGACAGCTATAACAATGGAGGAGGCGTACGTGACTTTGGTGGTGAGAGTGAAAGC
AATTTGGGAGGGCATGGAAGCTACAGTGATTTCTGAAAAAATAACAATCAATCTTAAAATTTGTACTCATGAAGGGAGGA
AACTTTGGAGGCAGAATCTCTGGCCCCTATGGTGGTGGAGACGAATACTTTGCCGAACCACATAACCAAGGTGGCTATGG
CAGTTCCAGCAAGAGCAGTAGCTATGGCAATGGCAGAAGATTT

Alignment

ORF - retro_mmul_1427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGG
          GK.RGF....F..H.SVDKIVIQKYHT.NGH.CEV.KAL..QEMAS.SSSQRG.SGSGNFGGG.GGGFGG
Retrocopy GKRRGFC---FYNHGSVDKIVIQKYHTGNGHHCEVKKAL**QEMASFSSSQRGCSGSGNFGGGCGGGFGG

Parental  NDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYG
          NDNFG..GNFS..G.FGGS.G.GGYGG..DGYNGFGND.GY.GG.PGYSGGSRGYGS.GQ..GNQGSGYG
Retrocopy NDNFGHRGNFSACGAFGGSCGDGGYGGN*DGYNGFGNDSGYEGGSPGYSGGSRGYGSSGQDSGNQGSGYG

Parental  GSGSYDSYNNGGG-GGFGGGSGSNFGGGGSYNDFGNYNNQSSN-FGPMKGGNFGGRSSGPYGGGGQYFAK
          G.GS.DSYNNGGG...FGG.S.SN.GG.GSY.DF...NNQS.N.F..MKGGNFGGR.SGPYGGG..YFA.
Retrocopy GGGSRDSYNNGGGVRDFGGESESNLGGHGSYSDF*KNNNQS*N<FVLMKGGNFGGRISGPYGGGDEYFAE

Parental  PRNQGGYGGSSSSSSYGSGRRF
          P.NQGGYG.SS.SSSYG.GRRF
Retrocopy PHNQGGYGSSSKSSSYGNGRRF

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	72.61 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	144.14 RPM
SRP007412_cerebellum	0.00 RPM	88.27 RPM
SRP007412_heart	0.00 RPM	141.68 RPM
SRP007412_kidney	0.12 RPM	70.66 RPM
SRP007412_liver	0.00 RPM	68.12 RPM
SRP007412_testis	0.08 RPM	87.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1427 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1427 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2285

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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,