RetrogeneDB ID: retro_mmul_2341

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:52233321..52234429(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.10169
• Ensembl ID: ENSMMUG00000011868
• Aliases: None
• Description: None

Sequence

>retro_mmul_2341
ATGGTCGCCCCGAGGTAGGTGGTCAACTTTGGACCTGGTACAACCAAGCTGCCACACTCAGTGTTGTTAGAGATGCAAAA
CGAATTATTACAAACAAAGGAATTGGCATTAGTGTTCTTGAAATGAGTTGCAGGTCGTTAGATTTTGCCAAGATTATTAA
CAATGCAGAGACTCTTGTGTGGGAATTGCTAGCTGTTCGAGACAACTACGAGGTGATTTTTGTGCAAGGAGGTGGGTCGA
GCCAGTTCAGTGCTGTCCCCTTAAAGCTGATTGGCTTGAAAGTAGGAAAGAGTGCGGCCTATGTGGTGACAAGAGCTTGG
TCAGCTAAGGCTGCAGAAGAAGCCAAGGAATTTGGGACTATAAATATTGTTCACTCTAAATTTGGGAATTATACAAAAAT
TCCAGATCCAAGCACCTGGAACCTCAACTCGGATGCCTCCTCCGTGTATTATCGCGCAAATGAGACGGTCCACGATGTGG
TGTTGGACTTTATAACCGATGTCAAAGGAGCAGTACTGGTTTGTAACATGCCCTCACACTTCCTGTCCAAGCCAGCGGAT
GTTTCCAAGTTTGGTGTGACTTTTGCTGGTGCCTAGAAGAACGCTGGCTCTGCGGGGGTCACCGTGGTGATTGTCAGTGA
TGACCAACTGGGGTTTGCCCTCCGAGAGTGTCCCTCGGTCCTGGAATACAAGGTGCAGGCTGGAAACAGCTCCTTGTATA
ACGTGCCTCCGTGTTTCAGCATCTACATCATGGGCTTGGTCCTGGAGTGGATTAAAAACAGTGGAGGTGCTGTGGCCATG
GAGAAGCTTAGCTCCATCAAATCCAAAATGATTTATGAGATTATTGATAATTCTCAAGGATTCTACGCATGTCCAGTGGA
GCCCCAAAATAGAAGCAAGATGAATATTCCATTCTGCATTGGCAATGTCAAAGGAGATGACGCTTTAGAAAAAAGATTTC
TCGATAAAGCTCTTGAACTCAATATGTTGTCCATGAAAGGGCATAGGTCTGTGGGAGGCATCCAGACCTCTCTGTATAAT
GCTGTCAAGATTGAACATGTTCGGAAGCTGGCTGCCTTCATGAAAAATTTTTGGAGATGCATCAGCTA

Alignment

ORF - retro_mmul_2341 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDAPRQVVNFGPGPAKLPHSVLLEMQKELLDYK-GIGISVLEMSHRSSDFAKIINNTETLVRELLAVPDN
          M.APR.VVNFGPG..KLPHSVLLEMQ.ELL..K.GIGISVLEMS.RS.DFAKIINN.ETLV.ELLAV.DN
Retrocopy MVAPR*VVNFGPGTTKLPHSVLLEMQNELLQTK<GIGISVLEMSCRSLDFAKIINNAETLVWELLAVRDN

Parental  YKVIFLQGGGSGQFGAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPST
          Y.VIF.QGGGS.QF.AVPL.LIGLK.G..A.YVVT.AWSAKAAEEAK.FGTINIVH.K.G.YTKIPDPST
Retrocopy YEVIFVQGGGSSQFSAVPLKLIGLKVGKSAAYVVTRAWSAKAAEEAKEFGTINIVHSKFGNYTKIPDPST

Parental  WNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTV
          WNLN.DAS.VYY.ANETVH.V..DFI.DVKGAVLVC.M.S.FLSKP.DVSKFGV.FAGA.KN.GSAGVTV
Retrocopy WNLNSDASSVYYRANETVHDVVLDFITDVKGAVLVCNMPSHFLSKPADVSKFGVTFAGA*KNAGSAGVTV

Parental  VIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQMIY
          VIV.DD.LGFALRECPSVLEYKVQAGNSSLYN.PPCFSIY.MGLVLEWIKN.GGA.AMEKLSSIKS.MIY
Retrocopy VIVSDDQLGFALRECPSVLEYKVQAGNSSLYNVPPCFSIYIMGLVLEWIKNSGGAVAMEKLSSIKSKMIY

Parental  EIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAV
          EIIDNSQGFY.CPVEPQNRSKMNIPF.IGN.KGDDALEKRFLDKALELNMLS.KGHRSVGGI..SLYNAV
Retrocopy EIIDNSQGFYACPVEPQNRSKMNIPFCIGNVKGDDALEKRFLDKALELNMLSMKGHRSVGGIQTSLYNAV

Parental  TIEDVQKLAAFMKN-FLEMHQL
          .IE.V.KLAAFMKN.FLEMHQL
Retrocopy KIEHVRKLAAFMKN<FLEMHQL

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	47.85 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	57.99 RPM
SRP007412_cerebellum	0.19 RPM	32.22 RPM
SRP007412_heart	0.00 RPM	2.30 RPM
SRP007412_kidney	0.00 RPM	64.79 RPM
SRP007412_liver	0.00 RPM	121.36 RPM
SRP007412_testis	0.00 RPM	12.06 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2341 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2341 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2341 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4054
Pongo abelii	retro_pabe_3328

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006898	1 retrocopy	retro_amel_375,
Bos taurus	ENSBTAG00000013960	1 retrocopy	retro_btau_1658,
Canis familiaris	ENSCAFG00000001570	1 retrocopy	retro_cfam_269,
Choloepus hoffmanni	ENSCHOG00000003817	1 retrocopy	retro_chof_2702,
Callithrix jacchus	ENSCJAG00000003319	1 retrocopy	retro_cjac_1203,
Echinops telfairi	ENSETEG00000004158	1 retrocopy	retro_etel_99,
Homo sapiens	ENSG00000135069	3 retrocopies	retro_hsap_2267, retro_hsap_4054, retro_hsap_412,
Gorilla gorilla	ENSGGOG00000015480	1 retrocopy	retro_ggor_407,
Loxodonta africana	ENSLAFG00000017917	2 retrocopies	retro_lafr_1249, retro_lafr_660,
Macaca mulatta	ENSMMUG00000011868	2 retrocopies	retro_mmul_1029, retro_mmul_2341 ,
Mustela putorius furo	ENSMPUG00000012566	1 retrocopy	retro_mputfur_808,
Nomascus leucogenys	ENSNLEG00000002989	3 retrocopies	retro_nleu_1010, retro_nleu_1288, retro_nleu_2805,
Oryctolagus cuniculus	ENSOCUG00000007765	1 retrocopy	retro_ocun_1092,
Pongo abelii	ENSPPYG00000019313	3 retrocopies	retro_pabe_1950, retro_pabe_308, retro_pabe_3328,
Pan troglodytes	ENSPTRG00000021045	2 retrocopies	retro_ptro_1606, retro_ptro_316,
Rattus norvegicus	ENSRNOG00000013971	1 retrocopy	retro_rnor_1663,
Tupaia belangeri	ENSTBEG00000012946	1 retrocopy	retro_tbel_1577,
Tarsius syrichta	ENSTSYG00000000093	2 retrocopies	retro_tsyr_1073, retro_tsyr_1212,