RetrogeneDB ID:

retro_mdom_843

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:180096105..180097648(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000014871
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NBN
Ensembl ID:ENSMODG00000007677
Aliases:None
Description:nibrin [Source:HGNC Symbol;Acc:7652]


Retrocopy-Parental alignment summary:






>retro_mdom_843
CCTTTGGAGTCTTTGAAAGCAAATTTAAATGTGTCTGGAAAAACTGTTTTAAATCAAGCTGTTTTACAACTTGGAGGACT
TATTGTAAACAACTGGACAGAAGAATGTACTCACCTTGTCATGGTGTCAGTTAAAGTTACTATTAAAACGATATGCGCTC
TGATTTGTGGTCGTCCTATTGTAAAACCAGATTATTTTACTGAGTTTCTCAAAGCCATTCGGACAAAGAAACGGCCTCCA
AAACTTGAAAGTTTTTATCCTCCCATTGATGAACCTGCTATAAATAATGAAAACCTGGATCTATCAAGTCGTAAGGAAAG
AAAACAAATATTCAGTGGGAAAACCTTTATATTTTTAAATGCCAAACAGCATAAGAAATTGAGTCCAGCAATTCTTCTTG
GAGGTGGAGAAGCTAAATTGGCAACAGAAGAAGATAAAGAAGCTGCTACTTCTTTTTTAACTCCTGGAACATGTGTTGTT
GATGCAGGATTAACAAATTCACAGGCTCTAGTGCCTGATTCTGTGAGAATCTGGATTCGTTCAATAATGGATATGCTTCA
AAGCCACCATCTTAGAGCCATCCCTGAAGCAGAAATTGGATTAGCAGTTATTTTCATGTCCACAGAGACTTACTGCAATC
CTGGTACAGGATTGGCTCTATCTCCAAGGCCACCAAGTCTTTCTCAAAACAAAATGGTAAATGAAACCTTAATGCCTGGT
GCCACAATGAATATCACTGCAGGTATTCCTGACACAGAATCAGAACAGGAAAATACTTGCTTGGATTTAAGTGAAAGTCC
AAAAGAGAATGAAACTCCTCAAGTGGAACAAAGATCCAAAGTATTTTCACAAGAAATGTTCACTGTAAAAGAGATTCCCA
ACACAAATTGTAGTGTTAATTTGGGAACAAAGCCACTTAATCAGACTTCAATAAAAACCCCAAACAGTCAACTGTCTCCA
AGTAAAATTTCAAGAAAAAGGAAAGAACAGGCTTCTCAAGAACAACAGACTAACTCCATTAAAAATTATTTCCAATCAGT
TTCAAAGAAAAGGGAAAGGAATGAAGAAGAACAAGAAGAATCTGTATCCAAATCTTCAAGGGTAGAGCTGTCTTGCTCTC
TTTTAGACCAAACCCAACCCACTACTTCCTCAGCATGGAGAAACCAGGAACAACACCAAACCCAGAAAGGACTCAATATG
TTGAACAAAAAAACAGATGAAACATATAGAAACACTAATCTAAAACTTAATGAAAATAGTCCTGTTGATGAACTTTTTAA
ATCCAACTCAAGAAAGAGGAAAGAACTGGATGATGTAGCTATGGAAAATGAGCATTTACATCAGGAACAAGAACAAGAGG
TTGAAATCGGAGTTCAAAGACCAGTGAATGGAATCAGTTTAGGAAAAAAACTGAGACTTGATATAAGAAAAAATGACTCT
GAAGATAATGAACCAACTCAAGAGAGTTGCAAAATAGTTCAAGAAAATGACCAGGAAAGAAATGTGAAGTTGAGCACAAA
CATTTTCTTCTGAAAAAGAACAG

ORF - retro_mdom_843 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.11 %
Parental protein coverage: 70.44 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPLVACPSCLDVSGKTVLNQAVLQLGGLIVNNWTEECTHLVMVSVKVTIKTICALICGRPIVKPDYFTEFL
PL......L.VSGKTVLNQAVLQLGGLIVNNWTEECTHLVMVSVKVTIKTICALICGRPIVKPDYFTEFL
RetrocopyPLESLKANLNVSGKTVLNQAVLQLGGLIVNNWTEECTHLVMVSVKVTIKTICALICGRPIVKPDYFTEFL
ParentalKAIRTKKRPPKLESFYPPIDEPAINNENLDLSSRKERKQIFSGKTFIFLNAKQHKKLSPAILLGGGEAKL
KAIRTKKRPPKLESFYPPIDEPAINNENLDLSSRKERKQIFSGKTFIFLNAKQHKKLSPAILLGGGEAKL
RetrocopyKAIRTKKRPPKLESFYPPIDEPAINNENLDLSSRKERKQIFSGKTFIFLNAKQHKKLSPAILLGGGEAKL
ParentalATEEDKEAATSFLTPGTCVVDAGLTNSQALVPDSVRIWIRSIMDMLQSHHLRAIPEAEIGLAVIFMSTET
ATEEDKEAATSFLTPGTCVVDAGLTNSQALVPDSVRIWIRSIMDMLQSHHLRAIPEAEIGLAVIFMSTET
RetrocopyATEEDKEAATSFLTPGTCVVDAGLTNSQALVPDSVRIWIRSIMDMLQSHHLRAIPEAEIGLAVIFMSTET
ParentalYCNPGTGLALSPRPPSLSQNKMVNETLMPGATMNITAGIPDTESEQENTCLDLSESPKEKETPQVEQRSK
YCNPGTGLALSPRPPSLSQNKMVNETLMPGATMNITAGIPDTESEQENTCLDLSESPKE.ETPQVEQRSK
RetrocopyYCNPGTGLALSPRPPSLSQNKMVNETLMPGATMNITAGIPDTESEQENTCLDLSESPKENETPQVEQRSK
ParentalVFSQEMFTVKEIPNTNCSVNLGTKPLNQTSIKTPNSQLSPSKISRKRKEQASQEQQTNSIKNYFQSVSKK
VFSQEMFTVKEIPNTNCSVNLGTKPLNQTSIKTPNSQLSPSKISRKRKEQASQEQQTNSIKNYFQSVSKK
RetrocopyVFSQEMFTVKEIPNTNCSVNLGTKPLNQTSIKTPNSQLSPSKISRKRKEQASQEQQTNSIKNYFQSVSKK
ParentalRERNEEEQEESVSKSSRVELSCSLLDQTQPTTSSAWRNQEQHQTQKGLNMLNKKTDETYRNANLKLNENS
RERNEEEQEESVSKSSRVELSCSLLDQTQPTTSSAWRNQEQHQTQKGLNMLNKKTDETYRN.NLKLNENS
RetrocopyRERNEEEQEESVSKSSRVELSCSLLDQTQPTTSSAWRNQEQHQTQKGLNMLNKKTDETYRNTNLKLNENS
ParentalPVDELFKSNSRKRKELDDVAMENEHLHQGTEQEQEVEIGVQRPVNGISLGKKLRLDIRKNDSEDNEPTQE
PVDELFKSNSRKRKELDDVAMENEHLHQ..EQEQEVEIGVQRPVNGISLGKKLRLDIRKNDSEDNEPTQE
RetrocopyPVDELFKSNSRKRKELDDVAMENEHLHQ--EQEQEVEIGVQRPVNGISLGKKLRLDIRKNDSEDNEPTQE
ParentalSCKIVQENE-PGKKCEVEH-ETFSSEKEQ
SCKIVQEN..PGKKCEVEH..TFSSEKEQ
RetrocopySCKIVQEND<PGKKCEVEH<QTFSSEKEQ

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_843 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_843 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 ENSMODG00000007677 1 retrocopy
retro_mdom_843 ,


Copyright © RetrogeneDB 2014-2017