RetrogeneDB ID: retro_mmul_386

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:84236832..84237519(+)
• Located in intron of: ENSMMUG00000002516

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSMMUG00000001858
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_mmul_386
ATGGAGGTTAAACTGCTGCCTGGTGGCTCCAAGCCCAATTCCGGCCATGGCTATCACCGCCAGGGGAAGGGGGTCATGAT
CCAAAGGAAACAGAGTAGGTGAGAAACTGTTTATTGGTGGTCTGAGCTTTGAAAAGACAGATGATAGCTTAAGAGAACAT
TTGCAAAAATGGGGCCCACTCACAGATTGTGTGGTAATGAGATACCCCCAAACAAAAAGTTCCAGGGGTTTGGTTTTATG
ACTCACTCTTGTGTTGAAGAGGTGGATGCAGCAACATGTACTCAACCACACAGGTTGGTGGGCATCTGTTGGAACCAAAG
AGAACTGTTTCTAGAAAGGATTCTATAAAGCCTGATGCCCATCTGACAGTGAAGAAAAATTTTGTTGGTGGTATTAAAGA
AGATACAGAAGAATATAATTTGAGAGACTACTTTGAAAAGTATGGCAAGATTGAAGCCATAGAAGTTATGGACGACAGGC
AGAGTGGAATAAAGAGAGAATTTGCTTTTGCAATTTTTGATGATCACGATACAGTTGATAACATTGTTGTTCAGGAATAC
CACACTATTAATGGGCATAATTGTGAGGTGAAAAGGCCCTTTCTGAACAAGAGATGCAGTCTGCTGGATCACAGAGAGGT
TGTGGAGGTGGATCTGGAATTTTATGGGTTGCAGAGGAAACTTTGGA

Alignment

ORF - retro_mmul_386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.22 %
• Parental protein coverage: 66.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MEVKPPPGRPQPDSGRRRRRRG-EEGHDPKEPEQLR-KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMR
          MEVK..PG...P.SG....R.G.E.GHDPKE.E..R.KLFIGGLSFE.TDDSLREH..KWG.LTDCVVMR
Retrocopy MEVKLLPGGSKPNSGHGYHRQG<EGGHDPKETE*VR<KLFIGGLSFEKTDDSLREHLQKWGPLTDCVVMR

Parental  DPQTKRSRG-FGFVTYSCVEEVDAAMCARPHK-VDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKED
          .PQTK.SRG.FGF.T.SCVEEVDAA.C..PH..V.G...EPKR.VSR.DS.KP.AHLTVKK.FVGGIKED
Retrocopy YPQTKSSRG<FGFMTHSCVEEVDAATCTQPHR<VGGHLLEPKRTVSRKDSIKPDAHLTVKKNFVGGIKED

Parental  TEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVK-KALSKQ
          TEEYNLRDYFEKYGKIE.IEVM.DRQSG.KR.FAF..FDDHDTVD.IVVQ.YHTINGHNCEVK.KALS.Q
Retrocopy TEEYNLRDYFEKYGKIEAIEVMDDRQSGIKREFAFAIFDDHDTVDNIVVQEYHTINGHNCEVK<KALSEQ

Parental  EMQSAGSQRGRGGGSG-NFMGRGGNFG
          EMQSAGSQRG.GGGSG.NFMG..GNFG
Retrocopy EMQSAGSQRGCGGGSG<NFMGCRGNFG

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	0.22 RPM	52.89 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	65.76 RPM
SRP007412_cerebellum	0.06 RPM	69.29 RPM
SRP007412_heart	0.00 RPM	49.99 RPM
SRP007412_kidney	0.00 RPM	50.70 RPM
SRP007412_liver	0.00 RPM	29.73 RPM
SRP007412_testis	0.04 RPM	153.30 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_386 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_386 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_450

---

Parental genes homology:

Parental genes homology involve 17 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Dasypus novemcinctus	ENSDNOG00000019022	3 retrocopies	retro_dnov_540, retro_dnov_711, retro_dnov_959,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
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,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,