RetrogeneDB ID:

retro_mdom_1753

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:7:215833812..215834567(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SMAD9
Ensembl ID:ENSMODG00000010017
Aliases:None
Description:SMAD family member 9 [Source:HGNC Symbol;Acc:6774]


Retrocopy-Parental alignment summary:






>retro_mdom_1753
AGCCACATGTTCTTGCCATCTCCCTGAACTTTAAGCTACCCCCTTCTGCAAGAAGTTCTTCTGGGCCAAGAAGTCCACAG
CAGTTCATAGTTGACACATTATCCCCACCTTATCATGCCGCAGAAACACCAGGTAGCCACAATGAATGTTCCTAATATGC
CACAGTTGATAGCCATTTAGTGTAGACACTGCCTAATAGATACACTAGACTGATTTGTTAGGAAGATCCTCAGCGGTGAT
GTTGGGCTATATACTATGAACTCAACAACCTAATCTGGAAGACTCTTTGGGCTCCTTCTAAAAGTATACTCATAGATGGA
TTTACAGATCATTCAAATAACAGGAACCCGTTCTGTCCTAGACTTCCTTCTAAGGTAAATGGAAACTTAACAATAGAAAA
CACTAAGAGACATGTAGGAAAGGATGTTCACCTGTATTTTGCTGGGGGGGAAGTTTATACTAAATGTGTGCTAGCAGCAT
TTTGTCAGAGTCATACCTGAAAGTATCAGCATGGCTTCTACCCAGCCACGGTCTGTAAGATTCCCAGTGACTGTGGCCTC
AAGATTTTCAACACTCAACTCTTTGTCCAGCTGCTGCAGTCAATAAATCATAGCTTTGAAGTAGTCTGTGAGTTGACTAA
GATATGCACTATTAGAATGTGTTTTGTTAAGGGCTGGGAAGCCGAACAACATCACTGGATATCCTTAGTATCCCTTGCTG
GACTGAAATACATCTCTCATGGACCATTGCATTAC

ORF - retro_mdom_1753 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.73 %
Parental protein coverage: 54.6 %
Number of stop codons detected: 6
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSHMFLPSPSTVSYP-HSPGSSSGPGSPYQLTVDTPPPPYHATETPGSHNGRPLDASADSHLVLSLPNGDF
SHMFLPSP.T.SYP..S..SSSGP.SP.Q..VDT..PPYHA.ETPGSHN.....A..DSHLV..LPN...
RetrocopySHMFLPSP*TLSYP<PSARSSSGPRSPQQFIVDTLSPPYHAAETPGSHNECS*YATVDSHLV*TLPNRYT
ParentalRPVCYEEPQHWCSVAYYELNNRVGETFQASSRSVLIDGFTDPSNNRNRFCLGLLSNVNRNSTIENTRRHI
R..C.E.PQ..C...YYELNN....T..A.S.S.LIDGFTD.SNNRN.FC..L.S.VN.N.TIENT.RH.
RetrocopyRLIC*EDPQR*CWAIYYELNNLIWKTLWAPSKSILIDGFTDHSNNRNPFCPRLPSKVNGNLTIENTKRHV
ParentalGKGVHLYYVGGEVYAECVSDSSIFVQSRNCNYQHGFHPATVCKIPSGCSLKIFNNQLFAQLLAQSVNHGF
GK.VHLY..GGEVY..CV.....F.QS....YQHGF.PATVCKIPS.C.LKIFN.QLF.QLL.QS.NH.F
RetrocopyGKDVHLYFAGGEVYTKCV--LAAFCQSHT*KYQHGFYPATVCKIPSDCGLKIFNTQLFVQLL-QSINHSF
ParentalEVVYELTKMCTIRMSFVKGWGAEYHR-QDVTSTPCWIEIHL-HGPLQW
EVV.ELTK.CTIRM.FVKGW.AE.H...D..S.PCW.EIHL.HGPL..
RetrocopyEVVCELTKICTIRMCFVKGWEAEQHH<LDILSIPCWTEIHL>HGPLHY

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_1753 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1753 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 ENSMODG00000010017 1 retrocopy
retro_mdom_1753 ,


Copyright © RetrogeneDB 2014-2017