RetrogeneDB ID: retro_mmul_1762

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:45007494..45008312(+)
• Located in intron of: ENSMMUG00000021377

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4422
• Ensembl ID: ENSMMUG00000020683
• Aliases: None
• Description: pre-mRNA-splicing factor RBM22 [Source:RefSeq peptide;Acc:NP_001244425]

Sequence

>retro_mmul_1762
AAAGCCACACTGACCAGTGACATGCTACTCAATCCAGCTTGGACCACACCCTCCTACCAAAGGAGTAAGCCCCACCTTTG
CTCCTTCTGGGTGAAAGAAGAGTGTAAGAGAGGAGAGGAATGTCTATGCAGACATAAGAAGCCTATAGATCCAGATGATC
TCCTTGCCGATCAGAATATTACACACAAATATTATGGAATCAATGATCCAGAAACAGATAAGCATCTAAAGTAGGCTTCA
ACCATGCCCCATCTGGACCCATCAGAGGACAAGGTTATCCTCACTATATGTTGGTAGTCTGGGTAATACCATTTCTGAGA
CAGATCTAAGACATCATCACTACCAGTTTGGAGAGATGCAGATGATTACTGTTGTTCAGAGAGAGCAGTGTGCTTTCATC
CAGGTTTCCACAGGGCAGTCTGCAGAAGTGGCTGCTGAGAAGTCCTTTAATAAGTTGATTGTCAATGGCTGTAGACTCAA
CATAAAATGGGGAAGATCCCAAGGATCCAGAGGAAAAGAAAAACAGAACAGATGGCAGACTCTGGGATCCAGCTACAGCC
TATTCCAGCACTGCCATGAGCTCTTCCTCTTCCTACAGCAGCAGAAGATGCATCTGCCAACTGCTTCAACCTGCCCCAAC
ATGGTCCTCCAGCTGTGGTGAACGCTGCCCACCAGCCACCAGCCCCTAGTCTTCTACACCCCTAACCCTAGGATTTAGGC
CACATATATTCACTTCAATGGGACCACCCCTTCCTTTCATGAGGACTCCAGGATTAATCCACTATCTATCTCATGACCCT
CAGAGGATGGGAAAACAT

Alignment

ORF - retro_mmul_1762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.59 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDP
          KAT.TSDMLL..A.TTP.Y.R..PH.CSFWVK.ECKRGEEC..RH.KP.DPDD.LADQNI...YYGINDP
Retrocopy KATLTSDMLLNPAWTTPSYQRSKPHLCSFWVKEECKRGEECLCRHKKPIDPDDLLADQNITHKYYGINDP

Parental  VADKLLKRASTMPRLDPPEDKTI-TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATR
          ..DK.LK.ASTMP.LD.P........LYVG.LG.TI.ETDLR.H.YQFGE...ITVVQR.QCAFIQ..T.
Retrocopy ETDKHLK*ASTMPHLD-PSEDKV>SSLYVGSLGNTISETDLRHHHYQFGEMQMITVVQREQCAFIQVSTG

Parental  QAAEVAAEKSFNKLIVNGRRLNV-KWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEEAS
          Q.AEVAAEKSFNKLIVNG.RLN..K.G.......K.K......DSGI.L.P.P.LP.ALP.P.AAE..AS
Retrocopy QSAEVAAEKSFNKLIVNGCRLNI<KMGKIPRIQRKRKTEQ-MADSGIQLQPIPALP*ALPLPTAAED-AS

Parental  ANYFNLPPSGPPAVVNIA-LPPPPGIAPPPP-PGFGPHMFHPMGPPPPFMRAPGPIHYPSQDPQRMGAH
          AN.FNLP..GPPAVVN.A..PP.P....P.P..GF.PH.F..MGPP.PFMR.PG.IHY.S.DPQRMG.H
Retrocopy ANCFNLPQHGPPAVVNAAHQPPAPSLLHP*P<LGFRPHIFTSMGPPLPFMRTPGLIHYLSHDPQRMGKH

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	34.06 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	25.54 RPM
SRP007412_cerebellum	0.06 RPM	41.39 RPM
SRP007412_heart	0.06 RPM	15.02 RPM
SRP007412_kidney	0.12 RPM	29.34 RPM
SRP007412_liver	0.00 RPM	11.20 RPM
SRP007412_testis	0.15 RPM	25.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1762 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1762 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1762 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3465
Pan troglodytes	retro_ptro_2348
Gorilla gorilla	retro_ggor_2337
Pongo abelii	retro_pabe_2861

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762 ,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,