RetrogeneDB ID: retro_mmul_1898

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:96569188..96570498(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1754
• Ensembl ID: ENSMMUG00000017569
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked [Source:RefSeq peptide;Acc:NP_001245264]

Sequence

>retro_mmul_1898
ATGAGTCATGTGGTGATGGAAAATGTGCTTTGGCTGGAGCAGCAGTTTTCTGGCCTAGACCTGGCCTCTTCAGATAATCA
GAATGGGGGAAGTACAGCCAGCAAAGGCCACTATATCCCTCTTTGTTAAGGAATAGAGCAGCTACTAAAGGATTCTACCA
TAAAGACAGTTTAGGGTGGTGTTCCAGCAAAGATAAGGATGCATAGAGCAGTTTTGAATCTCCTAATGATTCAAGTGCTA
ATTCTAGCTTCTTCAGTGATCATGGACGCGGATCGAGGGGAAGGTTTGATAATCATGGATGGAGTGATTATGATGGCACT
GACAGCCATGGTGACAGAAGTGGTTTTGGCAATTTATAACATGGTGGGAACAGTCACTGGTGTGACAAATAAGATGAAGA
GGATTGGTCAAAACCACTCCCCCCAAGTGAACGTTTGGAACAGGAACTCTTTTCTGGAGGCAACACTGGGATTAATTTTG
AGAAATATGGTGACATTCTAGTTGAGGCAACAGGCAGCAATTGTCCTCCACATGTTGAAAGTTTCAGTGATGTTGAGATG
GGAGAAACTATCATGGGAAACATGGAGGTTACTCATTATACTCGCCTGACTCCAGTGCAAAAGCATGCTCTTACTATTAT
AAAAGAGAAAAGAGACTTGACGGCTTGTGCCCAAACAGAGTCTGGAAAACTGCAGCATTTCTCTTGCCCATCTTGAGTCA
GATGTATTCAGATGGTCCAAAGGAGGCTTTGGGGGCCATGAAAGAAAATTAAAGGTGGGGACGCAGCAAACAATACCCAA
TCTTCTTGGTATTAGCACCAAGAAGAGAATTGGCAATACAGATCAATGAGAAAGCAGGAAAATTTTCATACTGATCTGGA
GTTCCTCCTTGCATGATTTATAGTGGTGCCGATATTGTTCAGCAGATTTGAGTCTTAGAAGGTGGATGGCACTTGTTAGT
AGCCACTCCAGGATATCTAGTGGATATGATGGAAAGAGGAAAGATTGGATTAAACTTTTGCGAATACTTCGTGTTAGAAG
AAGCTGATCAGATGTTGGATATGGGGTTTGAGCCTCAGATACATAGAAAAGTTGAACAAGATACTATGCCTCCAAAGGGT
GTCCACCACACTATGATGTTTAGTGCTACTTTACCTAAGGAAATACAGATGCTGGCTCATGACTTCTTTGATGAATATAT
TAGTATCTTCTTGGCTCTATACAGGAGTTGGCTGTACCTCTGAGAACATCACAAAGAAAGTAGTTTGGGTGGAAGAATCA
GACGAGCAGTTGTTTCTGCTTGACCTCCTA

Alignment

ORF - retro_mmul_1898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.95 %
• Parental protein coverage: 68.29 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSHVAVENALGLDQQFAGLDLNSSDNQSGGSTASKGRYIP-PHLRNREATKGFYDKDSSGWSSSKDKDAY
          MSHV..EN.L.L.QQF.GLDL.SSDNQ.GGSTASKG.YIP...LRNR.ATKGFY.KDS.GW.SSKDKDA.
Retrocopy MSHVVMENVLWLEQQFSGLDLASSDNQNGGSTASKGHYIP<SLLRNRAATKGFYHKDSLGWCSSKDKDA*

Parental  SSFGSRSDSRGKSSFFSDRGSGSRGRFDDRGRSDYDGIGSRGDRSGFGKFERGGNSRWCDKSDEDDWSKP
          SSF.S..DS...SSFFSD.G.GSRGRFD..G.SDYDG..S.GDRSGFG....GGNS.WCDK.DE.DWSKP
Retrocopy SSFESPNDSSANSSFFSDHGRGSRGRFDNHGWSDYDGTDSHGDRSGFGNL*HGGNSHWCDK*DEEDWSKP

Parental  LPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKH
          LPPSERLEQELFSGGNTGINFEKY.DI.VEATG.NCPPH.ESFSDVEMGE.IMGN.E.T.YTR.TPVQKH
Retrocopy LPPSERLEQELFSGGNTGINFEKYGDILVEATGSNCPPHVESFSDVEMGETIMGNMEVTHYTRLTPVQKH

Parental  AIPIIKEKRDLMACAQTGSG-KTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTREL
          A..IIKEKRDL.ACAQT.SG.KTAAFLLPILSQ.YSDGP.EAL.AMKEN.R.GR.KQYPI.LVLAP.REL
Retrocopy ALTIIKEKRDLTACAQTESG<KTAAFLLPILSQMYSDGPKEALGAMKEN*RWGRSKQYPIFLVLAPRREL

Parental  AVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDE
          A.QI.E.A.KFSY.S.V.PC..Y.GADI.QQI..LE.G.HLLVATPG.LVDMMERGKIGL.FC.Y.VL.E
Retrocopy AIQINEKAGKFSY*SGVPPCMIYSGADIVQQI*VLEGGWHLLVATPGYLVDMMERGKIGLNFCEYFVLEE

Parental  ADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEY--IFLAVGR-VGSTSENI
          AD.MLDMGFEPQI.R.VEQDTMPPKGV.HTMMFSAT.PKEIQMLA.DF.DEY..IFLA..R.VG.TSENI
Retrocopy ADQMLDMGFEPQIHRKVEQDTMPPKGVHHTMMFSATLPKEIQMLAHDFFDEYISIFLALYR>VGCTSENI

Parental  TQKVVWVEESDKRSFLLDLL
          T.KVVWVEESD...FLLDLL
Retrocopy TKKVVWVEESDEQLFLLDLL

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	157.99 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	78.93 RPM
SRP007412_cerebellum	0.00 RPM	162.99 RPM
SRP007412_heart	0.00 RPM	100.99 RPM
SRP007412_kidney	0.00 RPM	139.43 RPM
SRP007412_liver	0.12 RPM	61.71 RPM
SRP007412_testis	0.00 RPM	532.34 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1898 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1898 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035907	1 retrocopy	retro_btau_1846,
Callithrix jacchus	ENSCJAG00000009050	2 retrocopies	retro_cjac_1428, retro_cjac_4062,
Cavia porcellus	ENSCPOG00000013557	2 retrocopies	retro_cpor_326, retro_cpor_53,
Equus caballus	ENSECAG00000009901	1 retrocopy	retro_ecab_413,
Homo sapiens	ENSG00000215301	1 retrocopy	retro_hsap_4709,
Macaca mulatta	ENSMMUG00000017569	2 retrocopies	retro_mmul_1898 , retro_mmul_2504,
Mus musculus	ENSMUSG00000000787	1 retrocopy	retro_mmus_205,
Ornithorhynchus anatinus	ENSOANG00000011274	1 retrocopy	retro_oana_64,
Pongo abelii	ENSPPYG00000020257	1 retrocopy	retro_pabe_3657,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415,