RetrogeneDB ID: retro_mmul_2111

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:123903417..123904645(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4083
• Ensembl ID: ENSMMUG00000018871
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein K [Source:RefSeq peptide;Acc:NP_001253875]

Sequence

>retro_mmul_2111
GTGGAAACTGTACAGCCAGAAGAAACCTTCCCTAACACTGAAACCAATGGTGAATTTGGTAAATGCCCTGCAGAAGATAT
GGAATAGGACCAAGCATTGAAAGATCTAGAAACACTGATGAGATGGTTGAATTACGCATTCTGCTTCAGAGCAAGATTGC
TGGGGCAGTGATTGGAGAAGGAGGCAAGAATATCGAGGCTCTCTGTACGGACTACAATGCTAGTGTTTCAGTCTCAGACA
GCAGTGGCCCCGAGTGCATACTGAGTATCAGTGCTGATATTGAAACAATTGGAGAAATTCTGAAGAAAATCATCCCTAAC
TTGGAAGAGGACATGAAGTTGCCATTACTCACTGCAACCAGCCAGCTCCCGCTGGACTCTGATGCTGTTGAGTGCTTAAA
TTACCAACACTATAAAGGAAGTGACTTTGACTGCGAGTTGAGGCTGTTGATTCATCAGAGTCTAGCAGGAGGAATGTTGG
GGTCAAAGGTGCTAAAATCAAAGAACTTTGAGAGAACACTCAAACAACCATCAAACCTTTCTAGGAATGCTGTTCTCATC
CCACTGACAGAGTTGTTCTTATTGGAGGAAAACCGAATAGGGTTGTAGAGTGCATAAAGGTCATCCTTGATCTTATATCT
GAGTCTCCCATCAAAGGACCTGTACAGCCTTATGATCCCAATTTTTACAATGAAACCTATGATTATGGTGGTTTTGCAAT
GATGTTTGATGACCACCCTGGATGCCCAGTGGGATTTCCGATGTGGGGAAGAGGTGGTTTTGACAGAATGCCTCCTGGTC
GGGGTGGGCGTCCCATGCCTCCATCTAGAAGAGATATGAGCCCTCGTCGAGGATCACCTCCTCCTCCTCCTGGATGAGAT
GGCCGGGGTGGTAGCAGAGCTTGGAATCTTCCTCTTCCTCCACCACCACCACCTAGAGTGGGGAGACCTAATGGCCTGTG
ACAGAAGAGGGAGACCTAAAGACTGTTACGATGGCATGGTTGGTTTCAGTCCTGATGAAACTTGGAACTGTACAATAGAT
ACATGGAGCCCATCAGAATGGCAGATGCTTATGAACCACAGGATGGCTCCAGATATGATTATTCCCATGCAGGGGGTCGT
GGCTCATATGGTGATCTTGGTGGACCTATTATTACTATACAAGTAACTATTCCCAAAGATTTGACTGGATCTATTATTGG
CAAAAGTGGTCAGCAGATTAAACCTGTC

Alignment

ORF - retro_mmul_2111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.65 %
• Parental protein coverage: 89.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  METEQPEETFPNTETNGEFGKRPAEDMEEEQAFK-RSRNTDEMVELRILLQSKNAGAVIGKGGKNIKALR
          .ET.QPEETFPNTETNGEFGK.PAEDME..QA.K.RSRNTDEMVELRILLQSK.AGAVIG.GGKNI.AL.
Retrocopy VETVQPEETFPNTETNGEFGKCPAEDME*DQALK<RSRNTDEMVELRILLQSKIAGAVIGEGGKNIEALC

Parental  TDYNASVSVPDSSGPERILSISADIETIGEILKKIIPTLEEGLQLPSPTATSQLPLESDAVECLNYQHYK
          TDYNASVSV.DSSGPE.ILSISADIETIGEILKKIIP.LEE...LP..TATSQLPL.SDAVECLNYQHYK
Retrocopy TDYNASVSVSDSSGPECILSISADIETIGEILKKIIPNLEEDMKLPLLTATSQLPLDSDAVECLNYQHYK

Parental  GSDFDCELRLLIHQSLAGGI-IGVKGAKIKELRENTQTTIKLFQECCPHSTDRVVLIGGKPDRVVECIKI
          GSDFDCELRLLIHQSLAGG...GVKGAKIKEL.ENTQTTIK.F.ECC.H.TDRVVLIGGKP.RVVECIK.
Retrocopy GSDFDCELRLLIHQSLAGGM<VGVKGAKIKEL*ENTQTTIKPF*ECCSHPTDRVVLIGGKPNRVVECIKV

Parental  ILDLISESPIKGRAQPYDPNFYDETYDYGGFTMMFDDRRGRPVGFPMRGRGGFDRMPPGRGGRPMPPSRR
          ILDLISESPIKG..QPYDPNFY.ETYDYGGF.MMFDD..G.PVGFPM.GRGGFDRMPPGRGGRPMPPSRR
Retrocopy ILDLISESPIKGPVQPYDPNFYNETYDYGGFAMMFDDHPGCPVGFPMWGRGGFDRMPPGRGGRPMPPSRR

Parental  DYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPR-GGDLMAYDRRGRPGDRYDGMVGFSADETWDS
          D...MSPRRG.PPPPPG..GRGGSRA.NLPLPPPPPPR..GDLMA.DRRGRP.D.YDGMVGFS.DETW..
Retrocopy D---MSPRRGSPPPPPG*DGRGGSRAWNLPLPPPPPPR>WGDLMACDRRGRPKDCYDGMVGFSPDETWNC

Parental  AIDTWSPSEWQM-AYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQI
          .IDTWSPSEWQM.AYEPQ.GS.YDYS.AGGRGSYGDLGGPIIT.QVTIPKDL.GSIIGK.GQ.IK..
Retrocopy TIDTWSPSEWQM<AYEPQDGSRYDYSHAGGRGSYGDLGGPIITIQVTIPKDLTGSIIGKSGQQIKPV

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	247.97 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	204.27 RPM
SRP007412_cerebellum	0.32 RPM	252.68 RPM
SRP007412_heart	0.53 RPM	191.61 RPM
SRP007412_kidney	0.47 RPM	229.57 RPM
SRP007412_liver	0.20 RPM	128.37 RPM
SRP007412_testis	0.38 RPM	278.59 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2111 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2111 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3385

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021131	2 retrocopies	retro_btau_468, retro_btau_605,
Choloepus hoffmanni	ENSCHOG00000010832	2 retrocopies	retro_chof_1023, retro_chof_1589,
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Homo sapiens	ENSG00000165119	3 retrocopies	retro_hsap_2323, retro_hsap_2674, retro_hsap_3385,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macropus eugenii	ENSMEUG00000006975	3 retrocopies	retro_meug_271, retro_meug_357, retro_meug_484,
Microcebus murinus	ENSMICG00000015780	3 retrocopies	retro_mmur_1562, retro_mmur_235, retro_mmur_448,
Myotis lucifugus	ENSMLUG00000005871	2 retrocopies	retro_mluc_128, retro_mluc_561,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111 ,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Sus scrofa	ENSSSCG00000022760	1 retrocopy	retro_sscr_437,
Tupaia belangeri	ENSTBEG00000001289	1 retrocopy	retro_tbel_2491,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,