RetrogeneDB ID: retro_mmul_2398

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:46056419..46058022(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2141
• Ensembl ID: ENSMMUG00000009346
• Aliases: None
• Description: arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001248562]

Sequence

>retro_mmul_2398
GAGCTGTCTATAGGACCCTGCAAGTCACTACCCAATGTTCGAAGCCATTCCTCCTTCTGTTCCACACAGGTTCCACCATG
CACATTACCCAGACAAGAAATGGAGGTGGAAGTTTAAGTAACAAATTCCTCCTCCATTCCATCGACTCCCAGCACCAGCC
AGGAGGACCTTCAGATCGATAGTCCTCCCGGTGCCAACACACCCACACCTGTTCGCAAGGAGTCCAAGCACTGGTCCAAC
CTGTTGACATCTGAGAAAGGGAATGACCCAGATAAAGAAAGCCCTAGAGAGTCATGCTGACATCACTGGGAGCAGCAGGG
CCATTCCAATTAAACAGGGCATGCTCTTAAAGCTAAGTGGGAAATGGCTGAAGAAATGGAAAAAGAAATATGTCACCCTC
TGTGACAATGGCGTGCTCACCTATTATTCAAGCTTAGGTGATTATATGAAGAATATTCTTAAAAAAGAGATTGACCTTCG
GGTATCTACCATCGAAGTCCCAGGAAAGAGGCCACCCTTAGCCACACTGGCCTGTGTGCCCATTTCCAGCTCTAAAAGCA
ATGGCCTATCCAAGGACATGAACAGTCTATGTACCTCAGCCAATTCAGACACCGGGCTGGGTGACTCCATATGCTCCAGC
CCCAATATCTCCAGCACCACCAGCCCCAAGCTCAACCCACCCCCCTCTCCTCATACCAACAAAAAGAAACACCAAAGGAA
GAAAAGCACCAACAACTTGAAAGACGATGGCCTGTCCAGCACTGCTGAAGAAGAAGAAAACTTTATCATTGTGTCCCTCA
CTGGCCAAACGTGGCACTTTGAAGCCATGACATATGAGGAGCGGGATGCCTGGGTCCAAGCCATCGAGAGCCAGATCCTG
GCCAGCCTGCAGTCATGTGAGAGCAGCAAAAGCAAGTTCTGGCTGATGAGCCAGAGCGAGGCCATGGCCCTGCAGTCCAT
CAGAAACATGCGCGGGAACTCCCACTGTGTGGACTGTGAGACCCAGAATCCTAACTGGGCCACTTTGAATTTAGGAGTCC
TCGTGTGTATTGAATGCTCAGGGATCCACCATAATCTTGGCACCCACCTTTCCCGAGTTCAATCTCCGGACCTGGATGAC
TGGCCAGTCGAGCTCGTGAAGGTTATGTCATCTGTTGGCAATGAGCTAGCCAACAGCCTCTGGGAAGAGAGTAGCCAGGG
GCAGATGAAACCCTCGGTCGACTCCACAAGGGAAGAGAAGGAATGGTGGATCCATGCCAAATATGAGCAGAAGCTCTTCC
TGGCCCCACTACCCTGCACGGAGCTGTCCCTGGGCCAGCACCTGCTGCAGGCCACCACTGATGAGGACCTGCAGACAGCC
ATCCTGCTGCTGGCACATGGCTCCCGGGAGGAGGTGAACGAGACCTGTTGGGAGGGAGATGGCTGCACAGCGCTGCATCT
GGCCTGCTGCAAAGGGAATGTGGTCCTGGCTCAGCTCCTGATCTGGTACGGGGTGGATGTCATGGCCTGAGATGCCCATG
GGAACACAGCGCTAGCCTACGCCCAGCAGGCCTCCAGCCAGGAGTGCATCAAGGTACTGCTGCAGTACGGCTGCCCCGAC
GAG

Alignment

ORF - retro_mmul_2398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.66 %
• Parental protein coverage: 67.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLSIGPCKSLPNSPSHSSVCSAQV-SAVHISQTSNGGGSLSDY-SSSVPSTPSTSQKELRIDVPPTANTP
          .LSIGPCKSLPN..SHSS.CS.QV.S..HI.QT.NGGGSLS...SSS.PSTPSTSQ..L.ID.PP.ANTP
Retrocopy ELSIGPCKSLPNVRSHSSFCSTQV<STMHITQTRNGGGSLSNK>SSSIPSTPSTSQEDLQIDSPPGANTP

Parental  TPVRKQSKRRSNLFTS-RKGSDPDKEKKGLESRADSIGSGRAIPIKQGMLLKRSGKSLNKEWKKKYVTLC
          TPVRK.SK..SNL.TS.RKG......KK.LES.AD..GS.RAIPIKQGMLLK.SGK.L.K.WKKKYVTLC
Retrocopy TPVRKESKHWSNLLTS>RKGMT--QIKKALESHADITGSSRAIPIKQGMLLKLSGKWL-KKWKKKYVTLC

Parental  DNGVLTYHPSLHDYMQNVHGKEIDLLRTTVKVPGKRPPRATSACAPISSPKTNGLSKDMSSLHISPNSDT
          DNGVLTY..SL.DYM.N...KEIDL...T..VPGKRPP.AT.AC.PISS.K.NGLSKDM.SL..S.NSDT
Retrocopy DNGVLTYYSSLGDYMKNILKKEIDLRVSTIEVPGKRPPLATLACVPISSSKSNGLSKDMNSLCTSANSDT

Parental  GLGDSVCSSPSISSTTSPKLDPPPSPHANRKKHRRKKSTSNFKADGLSGTAEEQEENFEFIIVSLTGQTW
          GLGDS.CSSP.ISSTTSPKL.PPPSPH.N.KKH.RKKST.N.K.DGLS.TAEE.E....FIIVSLTGQTW
Retrocopy GLGDSICSSPNISSTTSPKLNPPPSPHTNKKKHQRKKSTNNLKDDGLSSTAEEEEN---FIIVSLTGQTW

Parental  HFEATTYEERDAWVQAIESQILASLQSCESSKNKSRLTSQSEAMALQSIRNMRGNSHCVDCDTQNPNWAS
          HFEA.TYEERDAWVQAIESQILASLQSCESSK.K..L.SQSEAMALQSIRNMRGNSHCVDC.TQNPNWA.
Retrocopy HFEAMTYEERDAWVQAIESQILASLQSCESSKSKFWLMSQSEAMALQSIRNMRGNSHCVDCETQNPNWAT

Parental  LNLGALMCIECSGIHRNLGTHLSRVRSLDLDDWPIELIKVMSSIGNELANSVWEESSQGRTKPSVDSTRE
          LNLG.L.CIECSGIH.NLGTHLSRV.S.DLDDWP.EL.KVMSS.GNELANS.WEESSQG..KPSVDSTRE
Retrocopy LNLGVLVCIECSGIHHNLGTHLSRVQSPDLDDWPVELVKVMSSVGNELANSLWEESSQGQMKPSVDSTRE

Parental  EKERWIRAKYEQKLFLAPLPCTELSLGQHLLRATADEDLRTAILLLAHGSRDEVNETCGEGDGRTALHLA
          EKE.WI.AKYEQKLFLAPLPCTELSLGQHLL.AT.DEDL.TAILLLAHGSR.EVNETC.EGDG.TALHLA
Retrocopy EKEWWIHAKYEQKLFLAPLPCTELSLGQHLLQATTDEDLQTAILLLAHGSREEVNETCWEGDGCTALHLA

Parental  CRKGNVVLAQLLIWYGVDVMARDAHGNTALAYARQASSQECIDVLLQYGCPDE
          C.KGNVVLAQLLIWYGVDVMA.DAHGNTALAYA.QASSQECI.VLLQYGCPDE
Retrocopy CCKGNVVLAQLLIWYGVDVMA*DAHGNTALAYAQQASSQECIKVLLQYGCPDE

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	0.90 RPM	32.05 RPM
SRP007412_brain_prefrontal_cortex	1.82 RPM	73.46 RPM
SRP007412_cerebellum	1.55 RPM	23.31 RPM
SRP007412_heart	0.59 RPM	6.89 RPM
SRP007412_kidney	1.06 RPM	14.79 RPM
SRP007412_liver	1.82 RPM	8.75 RPM
SRP007412_testis	4.71 RPM	5.13 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2398 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2398 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000157985	1 retrocopy	retro_hsap_604,
Macaca mulatta	ENSMMUG00000009346	1 retrocopy	retro_mmul_2398 ,
Nomascus leucogenys	ENSNLEG00000008562	1 retrocopy	retro_nleu_1923,