RetrogeneDB ID: retro_mmus_2793

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:130776114..130776974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rbm39
• Ensembl ID: ENSMUSG00000027620
• Aliases: Rbm39, 1500012C14Rik, 2310040E03Rik, B330012G18Rik, C79248, R75070, Rnpc2, caper
• Description: RNA binding motif protein 39 [Source:MGI Symbol;Acc:MGI:2157953]

Sequence

>retro_mmus_2793
ATTGTGTTAAACAGAAGATGTTTGATAAGGAAAACTCCATTCATGAAAGACAAGAGCCCTATGAGGGAAACTATTGATAA
TCTCACTCCTGAGGAAAGGGATGCAAGGGCAGTTTTCTGTGTGCAATTGGCAGCAAGAAGTCCACCAAGAGATTTGGAAG
AATTTTTTTCTACAGTAGAAAAGGTTCGAGTTGTGAGGATGATTTCTGATAGAAATTCAAGATGCTCAAAAGAATTGCCT
ATGTGGAATTTGTTGATGTCAGTTCAGTGCCTCTACCAAATAGATTAAATGGCCAATGAGTTTTAGGAGTGACAATAATA
GTCCAGACATCACAGCCAGAAAAAGACATAGCTGCTACAATGGTAAACAATTTTTAAAAAGGACTTATGAGGCTCTACTT
GTGCTTATTACACTTTAACATAACTGGAGAAATGCTTTAGGGGGATCTTTGAACCTATTGGAAGGATTGAAATTATTCAG
CTGCTGATGGATAATGAAACCAGTTGATCTAAGGGATATGGATTTGTTGCATTTTCTGACTAAGAATGTGCCCAAAAGGC
TTTGGAACAGTTTAATGGTTCGAGTTAGCTGAGAGACCACTGAAAGTTGGTCATATTTTTGGAAAAACTGATGCTTCTAG
TGCTAGTTCATTTTTGGACAGTGATGAACTACAAAGGACTGGAGTTGACTTGGGAACAACTAGACATCTTCAGGTACTGG
CAAGACTTGCAGAGGGTGCCTGATTGCAGATTCCACTTGCAGCACAAGTTTTACAAATGAGTGGCTTTTTGGTATTTGGT
GCTGGTAGATTTGCAACACCACTTTCAAGACAGACCAAAGCCTCAGATTTTGCTGCAGCT

Alignment

ORF - retro_mmus_2793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.53 %
• Parental protein coverage: 55.73 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IKLSRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISD
          I.L.RR....K.PF.KDKSP.RE.IDNLTPEERDAR.VFC.QLAAR..PRDLEEFFSTV.KVR.VRMISD
Retrocopy IVLNRRCLIRKTPFMKDKSPMRETIDNLTPEERDARAVFCVQLAARSPPRDLEEFFSTVEKVRVVRMISD

Parental  RNSRRS-KGIAYVEFVDVSSVPLAIGLTGQRVLGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGS
          RNSR.S.K.IAYVEFVDVSSVPL...L.GQ.VLGV.IIVQ.SQ.EK..AA.M.NN..KG....MRLY...
Retrocopy RNSRCS<KRIAYVEFVDVSSVPLPNRLNGQ*VLGVTIIVQTSQPEKDIAATMVNNF*KGL---MRLYLCL

Parental  LHFNITEDML-RGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNG-FELAGRPMKVG
          LHFNIT..ML.RGIFEP.GRIE.IQL.MD.ET..SKGYGF..FSD.ECA.KALEQ.NG.FELA.RP.KVG
Retrocopy LHFNITGEML>RGIFEPIGRIEIIQLLMDNETS*SKGYGFVAFSD*ECAQKALEQFNG<FELAERPLKVG

Parental  HVTERTDASSASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVADLQ
          H....TDASSASSFLDSDEL.RTG.DLGTT..LQ..ARLAEG..LQIP.AA.Q.LQMSG.L.FGA.....
Retrocopy HIFGKTDASSASSFLDSDELQRTGVDLGTTRHLQVLARLAEGA*LQIPLAA-QVLQMSGFLVFGA-GRFA

Parental  TRLSQQTEASALAAA
          T.LS.QT.AS..AAA
Retrocopy TPLSRQTKASDFAAA

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	173.63 RPM
SRP007412_cerebellum	0.00 RPM	164.96 RPM
SRP007412_heart	0.00 RPM	103.01 RPM
SRP007412_kidney	0.00 RPM	177.91 RPM
SRP007412_liver	0.00 RPM	90.75 RPM
SRP007412_testis	0.00 RPM	85.71 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2793 was not detected

EST

No EST(s) were mapped for retro_mmus_2793 retrocopy.

TSS

No TSS is located nearby retro_mmus_2793 retrocopy 5' end.

Lab

retro_mmus_2793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2793 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017535	1 retrocopy	retro_cjac_2199,
Homo sapiens	ENSG00000131051	1 retrocopy	retro_hsap_4679,
Macaca mulatta	ENSMMUG00000031284	1 retrocopy	retro_mmul_2491,
Mus musculus	ENSMUSG00000027620	3 retrocopies	retro_mmus_1512, retro_mmus_2792, retro_mmus_2793 ,
Otolemur garnettii	ENSOGAG00000011227	1 retrocopy	retro_ogar_267,
Ochotona princeps	ENSOPRG00000002183	2 retrocopies	retro_opri_55, retro_opri_913,
Pongo abelii	ENSPPYG00000010963	1 retrocopy	retro_pabe_3634,