RetrogeneDB ID: retro_mmul_2121

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:173789274..173790074(-)
• Located in intron of: ENSMMUG00000009041

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2803
• Ensembl ID: ENSMMUG00000003029
• Aliases: None
• Description: None

Sequence

>retro_mmul_2121
TTCAGCAACTCCATGTTTCACAACCATCACCTCTTCAAGGACAAGGTAGTGCTGGATGGGGGCACGGACACAAGCATCCT
CTGCATGTTCGCCGCCAAGGCCGGGCCCGCAACGTCATCGGGATCGAGTGGTTCCACTAGCTCTGAATATGCGGTGAAGA
TTGTCAAAGCCAACAAGTTAGACCACTTGGTGACCATCATCAAGGGGAAGGTGGCGGAGGTAGAGCTCCCGGTGGAAAAG
GTGGACATCATCATCAGCAAGTGGATGGGCTAACTGCCTCTTCTAGGAGTCCATGCTCAACACCGTGCTCCACGCCCTGA
CAAGTGACTGGCGCCCAATAAGCCTCATCTTCCCAGACCGGGCCACACTGTATGTGACGGTCATCGAGGACCGGCAGTAC
AAAGCCTACAAGATCCACAGGTGGGAGAACGCTTACGGCTTCGAAATGTCTTGCATCAAAGATGTGGCCATCAAGGAGCC
CCTAGTGGACCTCAAACAGCTGGTCAACAACGCCTGCCTCATAAAGGAGGTAGACATCTACACCGTCAAGGTGGAAGACC
TGACCTTCACCTCCCCGTTCTGCCTGCAAGTGAAACAGAATAACTACGTGCACGCCCAGGTGGCCTACTTCAACATCGAG
TTTATGCACTGCCACAGAGGACCTGGCTTTTCCATCAGCCCCGAGTCCCTGTACAAGCACTGGAAGCAGATGGTGTTTTT
ACATGGAGGACTACCTGACCTTGAAGACAGGCGAGGAGATCTTCAGCACCATCGGCATGTGGCCCAACGCCAAGAACAAT

Alignment

ORF - retro_mmul_2121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.85 %
• Parental protein coverage: 84.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YRNSMFHNRHLFKDKVVLDVGSGTGILCMFAAKAG-ARKVIGIEC-SSISDYAVKIVKANKLDHVVTIIK
          ..NSMFHN.HLFKDKVVLD.G..T.ILCMFAAKAG.AR.VIGIE..S..S.YAVKIVKANKLDH.VTIIK
Retrocopy FSNSMFHNHHLFKDKVVLDGGTDTSILCMFAAKAG<ARNVIGIEW>STSSEYAVKIVKANKLDHLVTIIK

Parental  GKVEEVELPVEKVDIIISEWMG-YCLFYESMLNTVLYARDKWLAPDGLIFPDRATLYVTAIEDRQYKDYK
          GKV.EVELPVEKVDIIIS.WMG..CLF.ESMLNTVL.A......P..LIFPDRATLYVT.IEDRQYK.YK
Retrocopy GKVAEVELPVEKVDIIISKWMG>NCLF*ESMLNTVLHALTSDWRPISLIFPDRATLYVTVIEDRQYKAYK

Parental  IHWWENVYGFDMSCIKDVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVH
          IH.WEN.YGF.MSCIKDVAIKEPLVD....KQLV.NACLIKEVDIYTVKVEDLTFTSPFCLQVK.N.YVH
Retrocopy IHRWENAYGFEMSCIKDVAIKEPLVDL---KQLVNNACLIKEVDIYTVKVEDLTFTSPFCLQVKQNNYVH

Parental  ALVAYFNIEFTRCHKRTGFSTSPESPYTHWKQTV-FYMEDYLTVKTGEEIFGTIGMRPNAKNN
          A.VAYFNIEF..CH...GFS.SPES.Y.HWKQ.V.FYMEDYLT.KTGEEIF.TIGM.PNAKNN
Retrocopy AQVAYFNIEFMHCHRGPGFSISPESLYKHWKQMV>FYMEDYLTLKTGEEIFSTIGMWPNAKNN

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	30.14 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	88.93 RPM
SRP007412_cerebellum	0.19 RPM	42.81 RPM
SRP007412_heart	0.24 RPM	51.47 RPM
SRP007412_kidney	0.23 RPM	34.04 RPM
SRP007412_liver	0.20 RPM	39.39 RPM
SRP007412_testis	6.86 RPM	27.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2121 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2121 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2121 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3406
Pan troglodytes	retro_ptro_2313
Gorilla gorilla	retro_ggor_2305
Pongo abelii	retro_pabe_2804
Callithrix jacchus	retro_cjac_1800

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003670	3 retrocopies	retro_cjac_1800, retro_cjac_1979, retro_cjac_764,
Danio rerio	ENSDARG00000010246	1 retrocopy	retro_drer_7,
Felis catus	ENSFCAG00000006081	1 retrocopy	retro_fcat_1762,
Homo sapiens	ENSG00000126457	1 retrocopy	retro_hsap_3406,
Gasterosteus aculeatus	ENSGACG00000004897	1 retrocopy	retro_gacu_2,
Gorilla gorilla	ENSGGOG00000000503	1 retrocopy	retro_ggor_2305,
Macaca mulatta	ENSMMUG00000003029	1 retrocopy	retro_mmul_2121 ,
Otolemur garnettii	ENSOGAG00000011938	2 retrocopies	retro_ogar_2471, retro_ogar_2929,
Rattus norvegicus	ENSRNOG00000026109	2 retrocopies	retro_rnor_1077, retro_rnor_2668,