RetrogeneDB ID: retro_mmul_1199

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:85053355..85054055(-)
• Located in intron of: ENSMMUG00000022023

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_1199
GGGAAAGCCACATCTACCAGTAACATGCTGGACAAACTGGCCTGGACCATACCTTATTACCTAAGGAATAAGCCCCACAT
TTGCTCCTTCTGGGTGGAGGGAAAGGTGAGAGAGGAGAGGAGTTTTGATAGAGACATGAGAAGCCTACAGGTCCACATGA
TTCCCTTGCTGATCAGATATTAAAGACCAATATTATACAGTCAATGACCCTGTAGCAGATAAGCTTCTATTGTAGGCTTC
AACCATGCCTCATCTGGAACTCCCAGAGGACAAGACTATCCCCACGCTAGTTGGTGATCCGGGTGATACCATTACTGAGA
CAGATCTTAAGAAATAATCTCTACCTATTTAGAGAGATCTGGACAATCCCTGTAGTGCAGAGACAACGGTGTGCATTCAT
CCAGGTTTCCACAGGGCAGGCTGCACAAGTAGCTGCAGAGAAGTCCTTTAATAAGTTCATCATCCATGGCTGCAGACTAA
GTGTAAAATGGGGAAGATCCCAGGCAGCCAGAGGAAAGGAAAATGACAGAACCCCAGACCCGGGGATGCAGATAGAGCCG
ATTCCAGTACTGCCGGGAACTCTTCCTCCTTCTGCAGCAGCAGATGCATCTGCCATGACTTCAGCCTACCTCCGAGTGCT
CCTACAGCTGTGGTGAACATTGCCTGGCCATGTTCAGCTGCTATTGCCCTGTCCTCACCC

Alignment

ORF - retro_mmul_1199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.08 %
• Parental protein coverage: 56.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GKATSTSDMLLKLARTTPYYKRNRPHICSFWVKGECK-RGEECPYRHEKPTDPDDPLADQ-NIKDRYYGI
          GKATSTS.ML.KLA.T.PYY.RN.PHICSFWV.G....RGEE...RHEKPT.P.D.LADQ..IKD.YY..
Retrocopy GKATSTSNMLDKLAWTIPYYLRNKPHICSFWVEGKVR<RGEEF**RHEKPTGPHDSLADQ<DIKDQYYTV

Parental  NDPVADKLLKRASTMPRLDPPEDKTITTLYVGGLGDTITETDL-RNHFYQFGEIRTITVVQRQQCAFIQF
          NDPVADKLL..ASTMP.L..PEDKTI.TL.VG..GDTITETDL.RN..Y.F.EI.TI.VVQRQ.CAFIQ.
Retrocopy NDPVADKLLL*ASTMPHLELPEDKTIPTL-VGDPGDTITETDL>RNNLYLFREIWTIPVVQRQRCAFIQV

Parental  ATRQAAEVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEE
          .T.QAA.VAAEKSFNK.I..G.RL.VKWGRSQAARGKE.....T.D.G...EP.P.LPG.LPP..AA...
Retrocopy STGQAAQVAAEKSFNKFIIHGCRLSVKWGRSQAARGKENDR--TPDPGMQIEPIPVLPGTLPPSAAAD--

Parental  ASA-NYFNLPPSGPPAVVNIALPPPPGIAPPPP
          ASA...F.LPPS.P.AVVNIA.P....IA...P
Retrocopy ASA<HDFSLPPSAPTAVVNIAWPCSAAIALSSP

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	0.12 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_1199 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1199 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4273
Pan troglodytes	retro_ptro_2898
Gorilla gorilla	retro_ggor_2859
Pongo abelii	retro_pabe_3486

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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,