RetrogeneDB ID:

retro_mdom_1162

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:297749337..297750124(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000021392
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBFD1
Ensembl ID:ENSMODG00000006727
Aliases:None
Description:ubiquitin family domain containing 1 [Source:HGNC Symbol;Acc:30565]


Retrocopy-Parental alignment summary:






>retro_mdom_1162
ATGGCGGCAGCCCGAGCCACGAATGACGACAGGGACTCAGGCATGGAACAAGATGCCCAGAAGCTACAGCTCAACTGTGT
AAACACCAAGGCTGAGACCACCTCCCTCGCCTCCTCATCGCCCTCTGCCTCAGCGACCAAGAGCAGCCTGCAGGCGGACC
AGTTGCTGGAGAATATAGCCAGTACCCAGGCCTCAGTCAGCAATGGCGACAACGCTGAATTGGAGAAGGAGCTGGTGGAT
CTGAAGATCATCTGGAACAAAAACAAGTATGACCTGCGAGTGCCTCTGGACAGCACCGGGGCGGAGCTGAAGCGCAGGAT
CCACTCCATTACAGGACTACCACCTGCCATGCAGAAAGTTATGTTTAAGAGACTTCTACCTGAGGAGAAAACATTACGGG
AAATCAAAGTGACCAGTGGTGCCAAGATTATGGTGGTTGGATCTACAATAAACGATGTTTTACACCCAAAGAGGCAGCAC
AGCAAGAAGCGAAAGCTGAAGAGAGTAAAAAGAAGCCACTTTGTAGGCAAAAGCAACACAGAACAGTATTAGATAAAGGG
AAACTTGAAGATTGATGCCTTCTGCTAAGAGTGCCCAGGAACAACTGCCAACAGTACCTTTATCAGGCATGTACAACGAG
AGAGGAGGAAAAGTAAGACTCACCTTTAAATTAGAACAAGACCAATTGTGGATTGTCCCTAAAGAGGGAGCTGAAAAATT
ATCCAGATGCTCCATTCAAAATTTGGTCAGTGAACCTATTGAAAGACATGAAGATCACCACATGATG

ORF - retro_mdom_1162 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.37 %
Parental protein coverage: 82.35 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAAAGAPDEVEEPGMETDAQKLQLNCVDAEAETSSCTSSSSSAPADKGSLQTDQPQENIATAQASVSNGD
MAAA.A.......GME.DAQKLQLNCV...AET.S..SSS.SA.A.K.SLQ.DQ..ENIA..QASVSNGD
RetrocopyMAAARATNDDRDSGMEQDAQKLQLNCVNTKAETTSLASSSPSASATKSSLQADQLLENIASTQASVSNGD
ParentalDAETEKELVDLKIIWNKNKYDVRVPLDSSGAELKRRIHSITGLPPAMQKVMFKGLLPEEKTLREIKVTSG
.AE.EKELVDLKIIWNKNKYD.RVPLDS.GAELKRRIHSITGLPPAMQKVMFK.LLPEEKTLREIKVTSG
RetrocopyNAELEKELVDLKIIWNKNKYDLRVPLDSTGAELKRRIHSITGLPPAMQKVMFKRLLPEEKTLREIKVTSG
ParentalAKIMVVGSTINDVLAVNTPKDAAQQEAKAEESK-KEPLCRQKQHRKVLDKGKPED-VMPSVKGAQERLPT
AKIMVVGSTINDVL....PK.......K....K.K.PLCRQKQHR.VLDKGK.ED..MPS.K.AQE.LPT
RetrocopyAKIMVVGSTINDVL---HPKRQHSKKRKLKRVK<KKPLCRQKQHRTVLDKGKLED<LMPSAKSAQEQLPT
ParentalVPLSGMYNKTGGKVRLTFKLEQDQLWIGTKERTEKLPMGSIKNVVSEPIEGHEDYHMM
VPLSGMYN..GGKVRLTFKLEQDQLWI..KE..EKL...SI.N.VSEPIE.HED.HMM
RetrocopyVPLSGMYNERGGKVRLTFKLEQDQLWIVPKEGAEKLSRCSIQNLVSEPIERHEDHHMM

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






(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
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1162 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1162 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 7 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000293312 retrocopies
Canis familiaris ENSCAFG000000176701 retrocopy
Callithrix jacchus ENSCJAG000000206141 retrocopy
Cavia porcellus ENSCPOG000000068722 retrocopies
Monodelphis domestica ENSMODG00000006727 2 retrocopies
retro_mdom_1162 , retro_mdom_1298,
Oryctolagus cuniculus ENSOCUG000000084441 retrocopy
Pongo abelii ENSPPYG000000071911 retrocopy



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