RetrogeneDB ID: retro_mmul_2504

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:73219631..73220713(+)
• 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_2504
CCCCAACAAGAGAATTGGCTGTACAGATATGAGGAAGCCAGAAAATTTTCATACCAGTGTAGAGTTCATCCTTGTGTAGT
TTATGGTGATGCTGATATTGGTCAACAAATTCAGGTCTTGGAACATGGATGCCACTTGTTAGTAGCCATGCCAGGACGTC
TAGTGGATTTGATGGAAAGAGGAAAGATTGGATTAGACTTCTGCAAATACTTAGTGTTGGATGAAGTTGATAGGATGTTG
GATACGGGATCTGGACCTCAGATACATTGTATACTTGAACAAGATACTATCCCACCAAAGGGCATTCATCACATCATGAT
GTTTAGTGCCACTTTTCCTAAGGAAATACGATGCTTGCTCGTGACTTTTTGGATGAATATATATTTTTGGCTGTAGGCAG
AGTAGGCTCTACCTCTGAAGTAGTTTGGGTGGAAGTAGTTTGGGTGGAAGAGCCAGATAAACGGTCATTTCTGCTTGATC
TCTTAAATGCACCAGGGAAGGATTCACTGACTTTAGAGTTTGTGGAGACAAAAAAGGGAGCAGATTCTCTGGAGAATTTC
TTATACCATGAAATATATCCTTGTACTAGTATTCATGGAGACCAATCACAGAGAGATCAAGACGGAGGCCCTTCACCAGT
TTTCCTTGGGGAAAAGTCCAATTCTAGTGGCTACAGCTGTGGCAGCATGAAGACTAGACATTTCAAATGTGAAACATGCT
TCAATTTTGATTTGCCAAGTGATATTGAAGAATATGTGCCTTGTATTGGCTGTACAGGATGTGTGGGAAACTAGGGCCTT
GCCATCTCATTCTTTAATGAAAGAAATATGAATATTACAAAGGATTTGCTGGATATTCTTGTAGAATTTAAACAAGAAGT
GCCTGCTTGATTGGAAAACATAGCTGATAAACACCACAAGGGTGGTATTCGTGCATGATCTAAAAGATTCAGTGGAGCAT
TTGGTGCCAGAGACTATTGACAACGTAGTGGTTCTGGCAGTTCTGGCTTTAGTAGTAGTCATACAAGCAGCAGCTGCAGT
GGTGGAGGTGGTCATGACATCAGCAGCAGATGTGGTAGAGGT

Alignment

ORF - retro_mmul_2504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.39 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKY
          P..E.....YEEARKFSY..RV.PCVVYG.ADIGQQI..LE.GCHLLVA.PGRLVD.MERGKIGLDFCKY
Retrocopy PQQENWLYRYEEARKFSYQCRVHPCVVYGDADIGQQIQVLEHGCHLLVAMPGRLVDLMERGKIGLDFCKY

Parental  LVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQ-MLARDFLDEYIFLAVGRVGSTS
          LVLDE.DRMLD.G..PQI..I.EQDT.PPKG..H.MMFSATFPKEI..MLARDFLDEYIFLAVGRVGSTS
Retrocopy LVLDEVDRMLDTGSGPQIHCILEQDTIPPKGIHHIMMFSATFPKEIR<MLARDFLDEYIFLAVGRVGSTS

Parental  ENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDRE-
          .............DKRSFLLDLLNA.GKDSLTL.FVETKKGADSLE.FLYHE.Y.CTSIHGD.SQRD...
Retrocopy XXXXXXXXXXXXPDKRSFLLDLLNAPGKDSLTLEFVETKKGADSLENFLYHEIYPCTSIHGDQSQRDQD>

Parental  EALHQFRSGKSPILVATAVAARGLDISNVKHV-INFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNI
          EALHQF..GKSPILVATAVAA..LDISNVKH...NFDLPSDIEEYV..IG.TG.VGN.GLA.SFFNERN.
Retrocopy EALHQFSLGKSPILVATAVAA*RLDISNVKHA<FNFDLPSDIEEYVPCIGCTGCVGN*GLAISFFNERNM

Parental  NITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSSRGRSKSSRFSGGFGARDYRQSSGASSSSFSSSRASS
          NITKDLLD.LVE.KQEVP..LEN.A..HH.KG..R..SK..RFSG.FGARDY.Q.SG..SS.FSSS..SS
Retrocopy NITKDLLDILVEFKQEVPA*LENIADKHH-KGGIRA*SK--RFSGAFGARDY*QRSGSGSSGFSSSHTSS

Parental  SRSGGGGHGSSRGFGGG
          S.SGGGGH..S...G.G
Retrocopy SCSGGGGHDISSRCGRG

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	1.46 RPM	157.99 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	78.93 RPM
SRP007412_cerebellum	1.94 RPM	162.99 RPM
SRP007412_heart	0.77 RPM	100.99 RPM
SRP007412_kidney	0.59 RPM	139.43 RPM
SRP007412_liver	0.36 RPM	61.71 RPM
SRP007412_testis	21.52 RPM	532.34 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2504 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2504 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2504 has 0 orthologous retrocopies within eutheria group .

---

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,