RetrogeneDB ID: retro_mmul_1962

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:98171591..98172131(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP43
• Ensembl ID: ENSMMUG00000009830
• Aliases: None
• Description: None

Sequence

>retro_mmul_1962
TGCTTGCTTATTGCTGTACCTGCTGCAGTTGCTTTCAGCTGGAGGAAATTTATGCTGTTTGTGTCTCAGAAAATCTGCAA
AACATGCTGGTGACCAGTGCCTCTGGGGAGCTTGAAGACTGCAGAGATGTTCTCTACGGGCTCTTGGGACAATGGGGAAA
ATTATGTTTCACTGCGGTCTATTGGAGATTTTGGAAACTTGAACTCTGATAGAGGGTTTGAAGGAGACAATCAATTACTG
TGTGATATTAGACACTATGGTGATATAATGGATTGACAGTTGTCTGACCAGGAAAGAATTGTAGCTGCTTCATCAACAGG
ATGTGTATCAGTTTTCCTTCATCATCTGAATAACCAGACTCTTTCAGTCAACCAGCTGTGAACTACAGCTCATTACCACA
CAGGCCCAGAAAGTCCTTCGTGTAGCAGTGCACCACGTACAGCTGTTGTGTGGAACAACCCAGAAATCATTAACGTTGGA
GACAATGGTTGAATAAATCTCTTCAAAGCTTATCACAAGGAAACCGAAAGAACTGTAGGC

Alignment

ORF - retro_mmul_1962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 73.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLLFAVPAAAAFGMEEIYAKFVSQKISKTRWRPLPSGSLQTAETFATGSWDNEENYVSLWSIGDFGNLDS
          CLL.AVPAA.AF........FVSQKI.KT.W.P.P.GSL.TAE.F.TGSWDN.ENYVSL.SIGDFGNL.S
Retrocopy CLLIAVPAAVAFSWRK-FMLFVSQKICKTCW*PVPLGSLKTAEMFSTGSWDNGENYVSLRSIGDFGNLNS

Parental  DGGFEGDHQLLCDIRHHGDVMDLQFFDQERIVTASSTGCVTVFLHHPNNQTLSVNQQWTTAHYHAGPGSP
          D.GFEGD.QLLCDIRH.GD.MD.Q..DQERIV.ASSTGCV.VFLHH.NNQTLSVNQ..TTAHYH.GP.SP
Retrocopy DRGFEGDNQLLCDIRHYGDIMD*QLSDQERIVAASSTGCVSVFLHHLNNQTLSVNQL*TTAHYHTGPESP

Parental  SYSSAPCTGVVCNNPEIVTVGEDGRINLFRADHKEAVRTIG
          S.SSAP.T.VV.NNPEI..VG..G.INLF.A.HKE..RT.G
Retrocopy SCSSAPRTAVVWNNPEIINVGDNG*INLFKAYHKETERTVG

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	0.45 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.48 RPM
SRP007412_cerebellum	0.00 RPM	1.03 RPM
SRP007412_heart	0.00 RPM	0.18 RPM
SRP007412_kidney	0.12 RPM	0.59 RPM
SRP007412_liver	0.00 RPM	0.24 RPM
SRP007412_testis	0.00 RPM	1.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1962 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009426	1 retrocopy	retro_chof_1765,
Cavia porcellus	ENSCPOG00000010815	1 retrocopy	retro_cpor_481,
Macaca mulatta	ENSMMUG00000009830	1 retrocopy	retro_mmul_1962 ,
Monodelphis domestica	ENSMODG00000016808	2 retrocopies	retro_mdom_199, retro_mdom_353,
Ictidomys tridecemlineatus	ENSSTOG00000013449	1 retrocopy	retro_itri_990,
Tarsius syrichta	ENSTSYG00000000944	1 retrocopy	retro_tsyr_267,