RetrogeneDB ID: retro_mmul_1330

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:29195764..29196727(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR45L
• Ensembl ID: ENSMMUG00000021803
• Aliases: None
• Description: None

Sequence

>retro_mmul_1330
GGCTGCCTTGCTTGCAGGATGGAAAATGGATTCTGAGTCTATAACACCAATCCATTAAAAGAAAAAGAGAAACAAAAATT
TCTAGGAGAAAGAGTTGGTCATAATGAAATGTTATTTTGCTGCAACTATTTAGCTTTAGTTGTTGGTGGAAAAAAGCCAA
AATACCTTCCCAACAAAGTGATGATCTGAGATGACTGAAAAAGGAGACTGTTAATGAAATAGAATTTGCTACAGAAATCA
AGGCAGTGAAATTGCAGCGAGATAGAATTGTGGTTGTTTTGGACTCCATGATTAAGGTGTTCACACTCACACAGAACTCC
CATCAGTTGTACATCTTTGAAACCTCCTGTAACCCTAAAGGCTGCTGTGTCCTCTGTCCTAATAGCAACAACTCTCTTCT
GGCCTTGCCAGGCAGGCACACAGGCCATGTGCAGCTCATGGACCAGGCCAGCACAGAGAAGCCACCTGTGGACATTCCCA
CTCCCGAGGGCATCCTGAGCTGCATCGCACTTAACCTGCAGGGAAAAGAATTGCAACCACACCCGAAAAGGGGACACTTA
TAAGAATATTTGATACTTCATCAGGACATTTAACCCAGGAGCTATGAAGAGGATCTCAAGCAGCTAATGTTTTCTGCATT
AGCTTCAATCAAGATGTGTCCTTCATTTGCATATCCAGTGACCACAGCACAGTGTACATTTTTGCAGCTGAGGACCCAGA
AAGGAATGAACAGTCCAACTTGGTGTCAGCTAGTTTCCTTCCAAAATCCTTTAGTTCCAAAGGGGTTTCTCCAAGTTTCA
GGTTCCCTTGGGCTCTCCATGCATTTGTGCCCTTGGAGCAGAGCCAAATGCAGTCACTGTGATTTGTGCAGACAGTGGCT
ACTACAAATTCCTATTCAACCCTAGAAGGGAATGCATCCCAGACATCTATGCACAGTTTCTAGAAATGATCTATGACAAG
CTG

Alignment

ORF - retro_mmul_1330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GCFACGMENGFRVYNTDPLKEKEKQEFLEGGVGHVEMLFRCNYLALVGGGKKPKYPPNKVMIWDD-LKKK
          GC.AC.MENGF.VYNT.PLKEKEKQ.FL...VGH.EMLF.CNYLALV.GGKKPKY.PNKVMI.DD.LKK.
Retrocopy GCLACRMENGF*VYNTNPLKEKEKQKFLGERVGHNEMLFCCNYLALVVGGKKPKYLPNKVMI*DD<LKKE

Parental  TVIEIEFSTEVKAVKLRRDRIVVVLDSMIKVFTFTHNPHQLHVFETCYNPKGLCVLCPNSNNSLLAFPGT
          TV.EIEF.TE.KAVKL.RDRIVVVLDSMIKVFT.T.N.HQL..FET..NPKG.CVLCPNSNNSLLA.PG.
Retrocopy TVNEIEFATEIKAVKLQRDRIVVVLDSMIKVFTLTQNSHQLYIFETSCNPKGCCVLCPNSNNSLLALPGR

Parental  HTGHVQLVDLASTEKPPVDIPAHEGVLSCIALNLQ-GTRIATASEKGTLIRIFDTSSGHLIQELRRGSQA
          HTGHVQL.D.ASTEKPPVDIP..EG.LSCIALNLQ.G.RIAT..EKGTLIRIFDTSSGHL.QEL.RGSQA
Retrocopy HTGHVQLMDQASTEKPPVDIPTPEGILSCIALNLQ<GKRIATTPEKGTLIRIFDTSSGHLTQEL*RGSQA

Parental  ANIYCINFNQDASLICVSSDHGTVHIFAAEDPKRNKQSSLASASFLPKYFSSKW-SFSKFQVPSGSPCIC
          AN..CI.FNQD.S.IC.SSDH.TV.IFAAEDP.RN.QS.L.SASFLPK.FSSK...FSKFQVP.GSPCIC
Retrocopy ANVFCISFNQDVSFICISSDHSTVYIFAAEDPERNEQSNLVSASFLPKSFSSKG<GFSKFQVPLGSPCIC

Parental  AFGTEPNAVIAICADGSYYKFLFNPKGECIRDVYAQFLEMTDDKL
          A.G.EPNAV..ICAD..YYKFLFNP..ECI.D.YAQFLEM..DKL
Retrocopy ALGAEPNAVTVICADSGYYKFLFNPRRECIPDIYAQFLEMIYDKL

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	35.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	47.12 RPM
SRP007412_cerebellum	0.13 RPM	36.29 RPM
SRP007412_heart	0.00 RPM	21.85 RPM
SRP007412_kidney	0.00 RPM	43.31 RPM
SRP007412_liver	0.08 RPM	19.12 RPM
SRP007412_testis	0.08 RPM	39.84 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1330 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1330 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1879
Gorilla gorilla	retro_ggor_1376
Pongo abelii	retro_pabe_1559

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005657	1 retrocopy	retro_cpor_322,
Homo sapiens	ENSG00000141580	2 retrocopies	retro_hsap_1820, retro_hsap_1879,
Gorilla gorilla	ENSGGOG00000006132	2 retrocopies	retro_ggor_1376, retro_ggor_2173,
Macropus eugenii	ENSMEUG00000013344	1 retrocopy	retro_meug_233,
Macaca mulatta	ENSMMUG00000010620	1 retrocopy	retro_mmul_1916,
Macaca mulatta	ENSMMUG00000021803	1 retrocopy	retro_mmul_1330 ,
Mus musculus	ENSMUSG00000025173	1 retrocopy	retro_mmus_1487,
Nomascus leucogenys	ENSNLEG00000010516	1 retrocopy	retro_nleu_1227,
Pongo abelii	ENSPPYG00000008785	2 retrocopies	retro_pabe_150, retro_pabe_1559,
Pan troglodytes	ENSPTRG00000009807	3 retrocopies	retro_ptro_1171, retro_ptro_1262, retro_ptro_2912,
Pteropus vampyrus	ENSPVAG00000006212	1 retrocopy	retro_pvam_158,