RetrogeneDB ID: retro_mmul_2506

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:74602540..74603551(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.9777
• Ensembl ID: ENSMMUG00000007450
• Aliases: None
• Description: RAF proto-oncogene serine/threonine-protein kinase [Source:RefSeq peptide;Acc:NP_001253231]

Sequence

>retro_mmul_2506
AAATCTCCAGGACCTCAGTGAGAAAGGAAGTCATCTGCATCCTCAGAAGACAGGAATCAAATGAAAATGCTTGGTAGACA
GGACTGGAACGATGATTGGGAGATTCCTGATGGGCAAATTACAGTGGGACAAAGAATTGGATCTAGATCATTTGGAACAG
TCTACAAGGGAAAGTGGCATGGTGATGTGGCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTATAAGCC
TTCAAAAATGAAGGAGGAGTGCTCAGGAAAACATAATATGTGAGTATCCTACTCTTCATGGGCTATTCAACAAAACCACA
ACTGGCTATTGTTACCCAGTGGTGTGAAGGCTCCAGCTTGTATTACCATCTCCGTATCATCGAGACCAAATTTGAGATGA
TCAAACTTACGGATATTGCACGACAGACTGCACAGGGCGTGGATTACTGACACGCCAAGTCAATCATCCATAGAGACCTC
AAGAGTAATAATATATTTCTTCATGAAGACCTCACAGTGAAAATGGGTGATTTTGGTCTAGCCACAGTGAAATCTCGATG
GAGTGGGTCCCATCAGTTTGAACAGTTGTCTAGATCCTTTTTGTGGATGTCACCAGAAGTCATCAGAATGCGAGATAAAA
ATTCATACAGCTTTCAGTCACATGTATATGCATTTGGGATTTTTCTATATGAACTGATGACTGGACAGTTACCTTATTCA
AACATCAACAACAGGGACCAGATAATTATTATGGTGGGATGAGGATACCTATCTCCAGATCTCAGTAAGGTACAGAGTAA
CTGTCAAAAAGCCATGAACAGATTAATGGCAGAGTGCCTTAAAAAGAAAAGAGATGAGAGACCACTCTTTCCCCAAATTC
TCACCTCTATTGAGCTGCTGACCCGCTCATTGCCAAAAATTCACCGCAGTGCATCAGAACTCTCTTTGAATTGGGCTGAT
TTCCAAACAGAGGATTTTAGTCTATATGCTTGTTCTTTGGCAAAAACACCC

Alignment

ORF - retro_mmul_2506 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.57 %
• Parental protein coverage: 51.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTPVPAQRERAPVSGTQEKNKIRPRGQRDSSYYWEIEASEVMLSTRIGSGSFGTVYKGKWHGDVAVKILK
          K.P.P.Q.ER.........N.....G..D....WEI.........RIGS.SFGTVYKGKWHGDVAVK.L.
Retrocopy KSPGP-Q*ERKSSASSEDRNQMKMLGRQDWNDDWEIPDGQITVGQRIGSRSFGTVYKGKWHGDVAVKMLN

Parental  VVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLIDI
          V..PTP.Q..AF.NE..VLRKT..V.ILLFMGY.TK..LAIVTQWCEGSSLY.HL...ETKF.M..L.DI
Retrocopy VTAPTPQQL*AFKNEGGVLRKT*YVSILLFMGYSTKPQLAIVTQWCEGSSLYYHLRIIETKFEMIKLTDI

Parental  ARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMAPEVIR
          ARQTAQG.DY.HAK.IIHRD.KSNNIFLHE.LTVK.GDFGLATVKSRWSGS.Q.EQ...S.LWM.PEVIR
Retrocopy ARQTAQGVDY*HAKSIIHRDLKSNNIFLHEDLTVKMGDFGLATVKSRWSGSHQFEQLSRSFLWMSPEVIR

Parental  MQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADC
          M.D.N..SFQS.VY..GI.LYELMTG.LPYS.INNRDQII.MVG.GY.SPDLSK...NC.KAM.RL.A.C
Retrocopy MRDKNSYSFQSHVYAFGIFLYELMTGQLPYSNINNRDQIIIMVG*GYLSPDLSKVQSNCQKAMNRLMAEC

Parental  VKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHRA-AHTEDIN--ACTLTTSP
          .KK...ERPLFPQIL.SIELL..SLPKI.RSASE.SL..A...TED....AC.L...P
Retrocopy LKKKRDERPLFPQILTSIELLTRSLPKIHRSASELSLNWADFQTEDFSLYACSLAKTP

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	1.12 RPM	57.26 RPM
SRP007412_brain_prefrontal_cortex	2.22 RPM	57.59 RPM
SRP007412_cerebellum	1.29 RPM	87.18 RPM
SRP007412_heart	0.71 RPM	64.72 RPM
SRP007412_kidney	1.06 RPM	71.24 RPM
SRP007412_liver	0.91 RPM	58.54 RPM
SRP007412_testis	23.67 RPM	35.39 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2506 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2506 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2506 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011807	1 retrocopy	retro_ecab_47,
Macaca mulatta	ENSMMUG00000007450	1 retrocopy	retro_mmul_2506 ,
Tarsius syrichta	ENSTSYG00000007438	1 retrocopy	retro_tsyr_1876,