RetrogeneDB ID:

retro_mdom_778

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:448193973..448195339(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FBXL5
Ensembl ID:ENSMODG00000001064
Aliases:None
Description:F-box and leucine-rich repeat protein 5 [Source:HGNC Symbol;Acc:13602]


Retrocopy-Parental alignment summary:






>retro_mdom_778
AAGGAATTCAAAGTTCATGAGCAGATTTAGAATGAATAACTATTGGCTTGCTTCAGTAATGCAGTCAGACCATTTATAAT
GTGCACTCTGACAACAAACTCCTTGAGATGCTTAGTCTCTTTGAGAAAGGATTGAAGAATGTAAAGAAAGAGTATGCTGA
GCTAAAAAATTATACAAAACAACTGGAGAGACTGGAAGATTTTACAAGAGATTTCCTTTCTCACCTGAAAGAAGAAGAGG
AAGTTTTTCATCCAATGTTAATGAAATATTTTACCTATGAAGAGCTGAAGGATATTAAAAAGAAAGAGACTGCACAACAT
TATTCTCACAAGGATACTGTGGAGCTTCTTAGAGGGCTTAGTCTCTGGAATCAAGCTGAAGAGAGAGAAGTTTTTTAAGT
ATTCTGTGGATGAAAAAAACAGATAAAGAAGCTGGAGTGCCAGATTACTCCACAAATATTACCCATATCCCTCCTGACGT
AATGCTGATGATTTTCAGTTACCTTAACCCTCAAGAGTTGTGTTGATGCAGTCAAGTTAACCCTAAATGGTCTCAATACA
CCCAAGCTGGATCTTTCTGGAAACATCTTTACCCTGTTCATGGGGCTAGAGGTGACTGATATAATGGTACAGGGATTGAA
CTTGATACTGAATCTGATGAGGAGTGGGTGAAAAATAGAAAAGATGAAAGTTGAGCTCTTCAGGAATGGGATAAAGATGC
TTTTATAGATGAGTCTGAAGAGCCCTCAGAAGAATCATCTGCCATAAATACTACAGAAAGGGAAAAACATTTTCTACATG
GCTTAATTCAAAATGTTCTCCAACATGTTGACACATATGTAAAAACTTTAGTATTAACATATACCTCTACAGTTTCTAGT
AAAGTGGTTTGACAGATTTTAGAACTTTACCCCAATCTGGAACATTTAAATCTTACCCAAACATACATCTCAGACTCTGC
ATTTGACATTTGGTCTTGGCTTGGTTGCTGTCAGAGTTTTGGACATCTTGATCCCTCAGGTTGTGAGAAAACCACCGACT
TGGCTATTAGAGAAGATTTCCAGAGCTTTGGGAATCCTGTCCTCTCATAAAGGTGGCATTCTGAAGACTTGCCAGAAACA
AAAGCACATCAACTACATGGAGAAGTAAAGATATTATTATGCAGTCTATTAGCAAATATACTTGTTTGCATGATATAACT
AATGAAAGTCTTGACAATGAAGTAGATAACTAATGACACTGGACTAAGCCTGTTTCTTCTGAAAATTTCAGTCCTGCTTA
TGTGTGAATGTTAAGATGCTGAATATTTGGCTAATATAGAAGATGCTGTAGAATGGAGATATAGAAATGTTGAAGGACTT
TCTGTA

ORF - retro_mdom_778 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.74 %
Parental protein coverage: 65.85 %
Number of stop codons detected: 12
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalKEFKMHEQIENEYI-IGLLQQRSRTIYNVHSDNKLSEMLSLFEKGLKNVKNEYEQL-NYAKQLKERLEAF
KEFK.HEQI.NE...IGLLQ..S.TIYNVHSDNKL.EMLSLFEKGLKNVK.EY..L.NY.KQL.ERLE.F
RetrocopyKEFKVHEQI*NE*L<IGLLQ*CSQTIYNVHSDNKLLEMLSLFEKGLKNVKKEYAELKNYTKQL-ERLEDF
ParentalTRDFLPHMKEEEEVFQPMLMEYFTYEELKDIKKKVIAQHCSHKDTAELLRGLSLWNQAEERQKFFKYSVD
TRDFL.H.KEEEEVF.PMLM.YFTYEELKDIKKK..AQH.SHKDT.ELLRGLSLWNQAEER..F......
RetrocopyTRDFLSHLKEEEEVFHPMLMKYFTYEELKDIKKKETAQHYSHKDTVELLRGLSLWNQAEEREVF*VFCG*
ParentalEK-TDKETEVPDYSTNITHLPPEVMLTIFSYLNPQELCRCSQVNTKWSQLAKTGSLWKHLYPVHWARGDW
.K.TDKE..VPDYSTNITH.PP.VML.IFSYLNPQELC.CSQVN.KWSQ....GS.WKHLYPVH.ARGD.
RetrocopyKK<TDKEAGVPDYSTNITHIPPDVMLMIFSYLNPQELC*CSQVNPKWSQYTQAGSFWKHLYPVHGARGD*
ParentalYNGPATELDTEPDEEWVKNRKDESRAFQEWDEDADIDESEESAEESLAINIAQMEKRLLHGLIQNILQHV
YNG...ELDTE.DEEWVKNRKDES.A.QEWD.DA.IDESEE..EES.AIN....EK..LHGLIQN.LQHV
RetrocopyYNGTGIELDTESDEEWVKNRKDES*ALQEWDKDAFIDESEEPSEESSAINTTEREKHFLHGLIQNVLQHV
ParentalGTSVKTLVLAYSSAVSSKMVRQILELCPNLEHLDLTQTDISDSAFDSWSWLGCCQSLRHLDLSGCEKITD
.T.VKTLVL.Y.S.VSSK.V.QILEL.PNLEHL.LTQT.ISDSAFD.WSWLGCCQS..HLD.SGCEK.TD
RetrocopyDTYVKTLVLTYTSTVSSKVV*QILELYPNLEHLNLTQTYISDSAFDIWSWLGCCQSFGHLDPSGCEKTTD
ParentalVA-LEKISRALGILSSHKGGILKTC-RNKSTSTSWRSKDITMQSTSKYACLHDITNESLSKEVDNERHWT
.A.LEKISRALGILSSHKGGILKTC.RNKSTST.WRSKDI.MQS.SKY.CLHDITNESL..EVDN..HWT
RetrocopyLA>LEKISRALGILSSHKGGILKTC>RNKSTSTTWRSKDIIMQSISKYTCLHDITNESLDNEVDN**HWT
ParentalKPVSSENFSSAYVWML-DAEDLADIEDAVEWRHRNVEGLSV
KPVSSENFS.AYV.ML.DAE.LA.IEDAVEWR.RNVEGLSV
RetrocopyKPVSSENFSPAYV*ML>DAEYLANIEDAVEWRYRNVEGLSV

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 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_778 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_778 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000001064 1 retrocopy
retro_mdom_778 ,


Copyright © RetrogeneDB 2014-2017