RetrogeneDB ID: retro_mmul_1553

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:29824247..29825058(+)
• Located in intron of: ENSMMUG00000029153

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_1553
ACAGACAGAACACAGCCAGTTGGTCGGCTGGGGAGAGTCACATACACCAGTGATGTGCTGTGCAAACTGGCACAGACCAC
ACCCTACTACCAAAGGAATAAGCACATTTGCTCCTTCTGGGTGAAAGAAGAGTGTGAGGGAGAAGAGGATGGCCCATACA
GACATGAGAAGCCTGCAGATCCAGATGACCCCCTTGCTGATAAGAATATTAAAGACTGATATGCAATCAATGACCCTGGA
GCAGATAAGCTTCTAAAGCAGGCTTCGCCATGCCTTGTCTGGATCCACCAGAGGACAAGGTTATCACCACACTCTTTGTT
GGTGATCTGGGTGATGCCATTACTGAGACAGATCTAAATAATCATTTCTAGTTATTTGAAGATCTGAATGATCACTACTG
TGCAGACCAGACAGTAGAGGGCTTTCATCCAGGTTTCCACAGGGCAGGCTGCAGAAGTGGCTGCAGAGAAATCCTTTAGT
AAGTTGATTGTCAAGGGCTGCAAACTCAGTGTAAAATGGAGAGGATCCCAAGCAGCCAGAGGAAAAGAAAAAGGACAGAA
CCACAGGCTGGGATCCAGCTAAGGCCTATTCCAGCACTTTCAGGAACAGAAACTCTTCCTCCTCCTCCTGCAGTAGCAGA
TATATCTGCCAACCACAGCAACCTACCCCCATGTGCTCCTCCAGCTGTGGTGAGCATTGCCTGGCCACCAGCCCCTGGTG
TCTCCTGCTGCTACCCCCAGGATTTCAGCCACCCATGTTCCATCCAATGGGACTATTGTCTTTCAAGAGGACTCCAGGAC
CAATACACTTT

Alignment

ORF - retro_mmul_1553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.35 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SDGTRPVGMLGKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQN
          .D.T.PVG.LG..T.TSD.L.KLA.TTPYY.RN..HICSFWVK.EC...E..PYRHEKP.DPDDPLAD.N
Retrocopy TDRTQPVGRLGRVTYTSDVLCKLAQTTPYYQRNK-HICSFWVKEECEGEEDGPYRHEKPADPDDPLADKN

Parental  IKDRYYGINDPVADKLLKRAS-TMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRT-ITVVQ
          IKD.Y..INDP.ADKLLK.AS..MP.LDPPEDK.ITTL.VG.LGD.ITETDL.NHF..F.......TV..
Retrocopy IKD*Y-AINDPGADKLLKQAS<AMPCLDPPEDKVITTLFVGDLGDAITETDLNNHF*LFEDLND>TTVQT

Parental  RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV-KWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGA
          RQ..AFIQ..T.QAAEVAAEKSF.KLIV.G..L.V.K..R......K.K........GI.L.P.P.L.G.
Retrocopy RQ*RAFIQVSTGQAAEVAAEKSFSKLIVKGCKLSV<KMERIPSSQRKRKRTE--PQAGIQLRPIPALSGT

Parental  --LPPPPAAEEEASANYFNLPPSGPPAVVNIALPPP-PGIAPPP-PPGFGPHMFHPMGPPPPFMRAPGPI
          ..LPPPPA.....SAN..NLPP..PPAVV.IA..PP.P...P...PPGF.P.MFHPMG....F.R.PGPI
Retrocopy ETLPPPPAVAD-ISANHSNLPPCAPPAVVSIAW-PP>PLVSPAA>PPGFQPPMFHPMG-LLSFKRTPGPI

Parental  HY
          H.
Retrocopy HF

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	0.00 RPM	41.39 RPM
SRP007412_heart	0.00 RPM	15.02 RPM
SRP007412_kidney	0.00 RPM	29.34 RPM
SRP007412_liver	0.00 RPM	11.20 RPM
SRP007412_testis	0.08 RPM	25.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1553 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1553 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1553 has 0 orthologous retrocopies within eutheria group .

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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,