RetrogeneDB ID: retro_mmul_1348

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:20421813..20422620(-)
• Located in intron of: None

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_1348
ATGGTGACCTCTCTGCATTTCCACACCTACAGCAGGAAGAATTGGGAAGAAGCAGACTTCCCCGTTCTGTGGTAGACACG
TCTTGCAGAAAACGCAGATATCCAAATAACCAAGGAAAAGCGTGGGAAGGAATGCAAAAGCTGTGCCAAACCATTCAGTG
TTTGGCTGGTGCCCTGGGGTTCACATGCATTTCAAGAAGACTGAAGGGTACCAAAGCTGCAGCAAATTAACTAATTTCTG
TCAGGCCTGCCTCTTAGTGGCAGAGTATGGCCCACCCATCCAGGTTCATGATGCAGGACTATCCTTAAAAGATGACATGC
CAAAGTTGGAGGTCAGCAAAAGTACTCCATTCAGAATACGGAAAGAGAGGTTTCCAACTCTGATGGAACACAGCCGGTTG
GTCTGCTGGGGAAAGCCACATCTAGCAATGATATGCTGAACAAACTGGCCCAGGCCATATCCTACCGCCTAAGAAATAAG
GCCCACATTTGCTCCTTCTGGATAAAAGGAGAGAGTGAGAGAAGAGAGGAGCGTCCATATAGACATGAGAGGCCTACACA
TCCAGATAATACCCTTGCTGATAAGAGTATTAAAGACCAGTATTACAGAATCAATGACCCTGGAGCTGGAGCATAGAAGC
TTCTAAGGCAGACTTTAAAAATGTGACATCTAGATCCACCAGAGGATAAGGCTATCACCTCACTATATGTTGATGGTCTG
GAGGGTATTATTTCTGAGACCAAGCTAACAAATCATCTCTACCTATGTGGAGAGATCTGGACGATCACTGTGCAGAGACA
GCAGTGT

Alignment

ORF - retro_mmul_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.41 %
• Parental protein coverage: 64.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEK-YGKECKICARPFTVFRWCPGVRMRFKKTE
          M.TSL...TY.R.NWE.ADFP.L..T.L.EN..I..TKEK..G...K.......VF.WCPGV.M.FKKTE
Retrocopy MVTSLHFHTYSRKNWEEADFPVLW*TRLAENADIQITKEK>VGRNAKAVPN-HSVFGWCPGVHMHFKKTE

Parental  VCQTCSKLKNVCQTCLLDLEYAGLPIQVRDAGLSFKDDMPKSDVNK-EYYTQNMEREISNSDGTRPVGML
          ..Q.CSKL.N.CQ.CLL..EY.G.PIQV.DAGLS.KDDMPK..V.K..Y..QN.ERE.SNSDGT.PVG.L
Retrocopy GYQSCSKLTNFCQACLLVAEY-GPPIQVHDAGLSLKDDMPKLEVSK<KYSIQNTEREVSNSDGTQPVGLL

Parental  GKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGIND
          GKATS..DML.KLA....Y..RN..HICSFW.KGE..R.EE.PYRHE.PT.PD..LAD..IKD.YY.IND
Retrocopy GKATSSNDMLNKLAQAISYRLRNKAHICSFWIKGESERREERPYRHERPTHPDNTLADKSIKDQYYRIND

Parental  PVAD--KLLKRASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC
          P.A...KLL.....M..LDPPEDK.IT.LYV.GL...I.ET.L.NH.Y..GEI.TIT.VQRQQC
Retrocopy PGAGA*KLLRQTLKM*HLDPPEDKAITSLYVDGLEGIISETKLTNHLYLCGEIWTIT-VQRQQC

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	0.00 RPM	25.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1348 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1348 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1594

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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,