RetrogeneDB ID:

retro_mmus_3654

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:84018248..84018897(-)
Located in intron of:ENSMUSG00000045103
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Psmf1
Ensembl ID:ENSMUSG00000032869
Aliases:Psmf1, AW048666, BC012260, PI31
Description:proteasome (prosome, macropain) inhibitor subunit 1 [Source:MGI Symbol;Acc:MGI:1346072]


Retrocopy-Parental alignment summary:






>retro_mmus_3654
ATGGTGGCCTTGGAAGTTCTCTTTGCATCAGCCATTCTGACCATGAGCTGCCCTCAGGACTTCCTCATCTGTTTCCTGCA
CTATGAAGTGGTGCCAAAGGCTAATATTGCTTGGGCACCAGCGAGCAGCCAAATCCCAGTAGTAAGTGAGAATGACTGCT
AGCAACATGGAAGAGCAATATAAGAACTGTCCTCCAGTATGAATCTAAGGATGGAGCCAGGAAAATACTTTTTGAAAGCT
GTCTCTGTGGAGAATGGCATGATCATCAATGTGCTGGAACATGATACACAGAAGGGGCCAGATTAGATTCCTAACCTAGA
TGATTATACTAATGTATAAGATCAAAGTAATTTCCACAGGATCTATAAGAACAGTGAAGAGATTCAGTCTTGGATTAGAT
CTGAAATTATCACACCTACCTGAGAGCATAGGAGAAGGCTCTTATAAGCAATGTCCATCTGGAGGTCCTATCAGCCACCA
TCAGAGAGGTAAACCCACTCAAGAATGCCTCACACCATTCTCATACTAACCAGCAGCCCTTTTGGTGTGGTCCACTGAAT
CCATTTGCTGTCTTGAGAAGATCTAGACCCCCTATTGGTGTCAGCGAGTTGGAATAATTATGGATCCCCTGAGATTTTTG
CTTCCCAAA

ORF - retro_mmus_3654 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.3 %
Parental protein coverage: 80.81 %
Number of stop codons detected: 6
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMAGLEVLFASAAPSMSCPQDALVCFLHWEVV-TNGYYALGTGDQPGPSDKKSELLPAKWNSNKELYALRY
M..LEVLFASA...MSCPQD.L.CFLH.EVV...G.Y.LGT..QP.PS.K...LL.A.W.SN.....L.Y
RetrocopyMVALEVLFASAILTMSCPQDFLICFLHYEVV<AKG*YCLGTSEQPNPSSK*E*LL-ATWKSNIRT-VLQY
ParentalESKDGARKLL-LKAVSVENGMIINVLELGTQQVADLTLNLDDYIDAEDLSDFHRTYKNSEELRSQIRSGI
ESKDGARK.L.LKAVSVENGMIINVLE..TQ...D...NLDDY....D.S.FHR.YKNSEE..S.IRS.I
RetrocopyESKDGARKIL>LKAVSVENGMIINVLEHDTQKGPD*IPNLDDYTNV*DQSNFHRIYKNSEEIQSWIRSEI
ParentalITPIHEQW-EKARANSPPREFPPATAREVDPLQISSHRPHTSRQPAWRDPLSPFAVGGDDLDPFG-CQRG
ITP..E...EKA.......E...AT.REV.PL...SH..HT..QP.W..PL.PFAV......P.G.CQR.
RetrocopyITPT*EHR<EKALISNVHLEVLSATIREVNPLKNASHHSHTNQQPFWCGPLNPFAVLRRSRPPIG<CQRV
ParentalGMIVDPLRSGFPR
G.I.DPLR...P.
RetrocopyGIIMDPLRFLLPK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 27 .73 RPM
SRP007412_cerebellum 0 .00 RPM 27 .49 RPM
SRP007412_heart 0 .03 RPM 15 .81 RPM
SRP007412_kidney 0 .00 RPM 22 .93 RPM
SRP007412_liver 0 .00 RPM 25 .51 RPM
SRP007412_testis 0 .00 RPM 319 .53 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3654 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3654 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3654 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3654 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3654 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000032869 1 retrocopy
retro_mmus_3654 ,


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