RetrogeneDB ID:

retro_mdom_1138

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:220386180..220387356(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC170
Ensembl ID:ENSMODG00000016728
Aliases:None
Description:coiled-coil domain containing 170 [Source:HGNC Symbol;Acc:21177]


Retrocopy-Parental alignment summary:






>retro_mdom_1138
GAAGGCACTGAGGCAGAAAAGAAAGCTATTTCTCTTCTTTCTAAGTTATGAAATTAACTACAAACTGATAAGCCATTGCT
GCCTTTGCATGATAACTAGGTTGATACTGATATATGGAACCAATACCTGGAAGATTAACATAGTCTTTTAGATGAAAATG
ACAAAAAAAATAAGCTGGTTTCAATCTTCTTGGTTGTATGTAGAGTGTTATTTATACTGTAGAATTCATGAAGCATTAGT
GTTAAGTTCACTTTGTGACTTAAGTGACTTTGGTGTATTTAAAGACTCAAAAGACCAGAATTTTTTAGAATCACGGGGTG
CTATTGAGGCTTTATGTTTTTATCTACAAGAGTCAAAAAGAACGATTGAAGTTGTAGAGGAAAATATACAAAAGATGAAT
TTGTCTTGCAGATTATGTTATGGTGAAATAAGTGTGATCTGGCAGTTGTACCTGGTCAGAGCATCCCTCAAACATCTAGT
CCACTAACCATTTTGGAAGGCCTAAAACCTTTCATTTTAGTGAATAATATGGATACCCTTTGGTCACTACTTTTAAACAA
AAGGAAAAAGAGTCAGGAGAATTTTTCTGTTATTAGAGTGGATTTTATCCTGGATAATGCAAGGTTTGAACTTGTTATGG
ATTTGGTAATGGCAGACTTCCTGATAGCCTCAAACTTGGCTACTGAAATCCATTTCCATGGAAAATGTACTCCATGGTTT
GTTTCAGATACTAATAGAAAAGACGTGAATTGGTTGATTACACAATTAAAAGCTGCTGAGAGCATGTGCCTGTCTACTTT
AGGGCTTATCTGGGAGGACTATCTTAAAAACAATACATGGGTTTACCACGATCATATGTTTTGGACTCTGTCTTTTGAAC
ATTGTTCTATGCCTCATGTTGCTCCTGACTTATATGCTGATCTACAAAAGTCAAATTTAATTCTTTTCAAAGGTGATTTG
AACTATAGGAAATTGTTAGGAGACAGAAAATGGGGGTTTACAATTCCATTTCATGAGGCTTTAAATGGCTTCCATCCTTC
ACTTCTCTGTAGCATAAAAATAGTAAAAACTCAAGTTTAAGCTGGTCTAGCCCCTGGGCAAGGAGAACAAGTTGCAAATT
CTAATCCTGAATGGATGACCAGTGGAAACTCTGGTTTATTACAGTTTTATGGAGGG

ORF - retro_mdom_1138 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.38 %
Parental protein coverage: 88.69 %
Number of stop codons detected: 6
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalEGTEAEKKAISLLSKLRNELQTDKPLLPLHDDWVDTDIWNQYLEDQHNLLNENDKKI-SWFQSSWLYVEC
EGTEAEKKAISLLSKL.N.LQTDKPLLPLHD..VDTDIWNQYLED.H.LL.END....SWFQSSWLYVEC
RetrocopyEGTEAEKKAISLLSKL*N*LQTDKPLLPLHDN*VDTDIWNQYLED*HSLLDENDXXX>SWFQSSWLYVEC
ParentalYLYRRIHEALVLSS--PISDFDVFKDSKDQNFLESRGAIEALCFYLQESKRTIEVVDENIQK-DEFCKLL
YLY.RIHEALVLSS....SDF.VFKDSKDQNFLESRGAIEALCFYLQESKRTIEVV.ENIQK.DEF...L
RetrocopyYLYCRIHEALVLSSLCDLSDFGVFKDSKDQNFLESRGAIEALCFYLQESKRTIEVVEENIQK<DEF--VL
ParentalQIMLWGNKCDLAVVPGQSIPQTSSPLTILEGLKPFILVNNMDALWSLLLNKRKKSQENFSVIRVDFILDN
QIMLW.NKCDLAVVPGQSIPQTSSPLTILEGLKPFILVNNMD.LWSLLLNKRKKSQENFSVIRVDFILDN
RetrocopyQIMLW*NKCDLAVVPGQSIPQTSSPLTILEGLKPFILVNNMDTLWSLLLNKRKKSQENFSVIRVDFILDN
ParentalAGFELVTDLVMADFLIASNLATEIHFHGKCIPWFVSDTNIKDVNWLITQLKAAESTYLSTCGLIWEDYLK
A.FELV.DLVMADFLIASNLATEIHFHGKC.PWFVSDTN.KDVNWLITQLKAAES..LST.GLIWEDYLK
RetrocopyARFELVMDLVMADFLIASNLATEIHFHGKCTPWFVSDTNRKDVNWLITQLKAAESMCLSTLGLIWEDYLK
ParentalKKTWVYHDHMFWTLPFEYCAMPHVAPDLYADLQKSNLILFKGDLNYRKLLGDRKWGLTIPFHEALNGFHP
..TWVYHDHMFWTL.FE.C.MPHVAPDLYADLQKSNLILFKGDLNYRKLLGDRKWG.TIPFHEALNGFHP
RetrocopyNNTWVYHDHMFWTLSFEHCSMPHVAPDLYADLQKSNLILFKGDLNYRKLLGDRKWGFTIPFHEALNGFHP
ParentalAPLCSIRTVKTQVQAGLAPGQGEQVADSNPEWMTSGNYGILQFDGG
..LCSI..VKTQV.AGLAPGQGEQVA.SNPEWMTSGN.G.LQF.GG
RetrocopySLLCSIKIVKTQV*AGLAPGQGEQVANSNPEWMTSGNSGLLQFYGG

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_1138 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1138 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 ENSMODG00000016728 1 retrocopy
retro_mdom_1138 ,


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