RetrogeneDB ID:

retro_mdom_1409

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:338827823..338829440(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000002674
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT7
Ensembl ID:ENSMODG00000025055
Aliases:None
Description:UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) [Source:HGNC Symbol;Acc:4129]


Retrocopy-Parental alignment summary:






>retro_mdom_1409
ATGAGGCTGAAGATCGGGTTCATCTTATGCAGTTTGCTGGTGGTAGGAAGCTTTCTGGGGCTGGTGGTGCTTTGGTCCTC
CCTGTCCCCCCGGCCTGACGGCCAGAACCCGCTCAATGGGATGAGGGAAGGCAGAGACCTCAACGTTCCCATCCCTATCA
GAGGAGGCAATGGATTGGCCCCTGGGGGCGACAGATTCAAACCTGTGGTGCCCTGGCCCCATGTGGAAGGGGTGGAAGTG
GACTTGGAGTCTATTAGAAGAAAAAACAAAGCCAAAAATAAACAAGAGCACCACGCTGGGGGTATCAACCAGCAAAATGC
CCTCCAGAGACAGACAGTATCTCACTCTTAAGCCTCAGACACTTACCTACCATGATCCTGTGCTCCGTCTGGGAATCATT
GGTAATTTTGAACCCAAAGAACCGGAACCTCATGGTGTTCTCCGTGGCCCTGGAGAGGAAGCAAAGCCATATGTTTTGGG
ACCAGATTACAAAGAGTCCATTCATGCCAGCATTAAAGAGTTTGGATTTAACATAGTGGCCAGTGATATGATCTCACTGG
ACCGCAGCATCAATGATTTGCAACAAGAAGAATGCAAGTATTGGCATTATGATGAAAACCTGCTCATTTCCAGTGTTGTC
ATTGTCTTCCATAATGAAAGATGGTCAACTCTTATGAGAACAGTTCACAGTATAATTAAAAGGACACCAAGGAAATATTT
GGCAGAAATTGTGTTAATTGATGATTTTAGTAATAAAGCACTCTTAAAAGAGAGACTAGATGACTACATTAAGCAGTGGA
ATGACCTGGTGAAGGTATTTCGAAATGAGAGACGAGAAGGTTTAATTCAGGCTCGAAGTATTGGAGCACACAAGGCTAAA
CTTGGACAGGTTCTGATATACCTTGATGTCCACTGTGATGTGGCAGTAAACTGGTATGCCCCGCTTGTGGCTCCTATATC
TAAAGACAGAACCGTTTCCACTGTGCTGATTATAGATATCATAGATGGCAACAATTTTAAAATTATGCCCCAAGGGGGTG
GTGATGAAGATGGGTACACTCGAAGAGCGTGGGATTGGAGTTTGCTCAGGAAGAGAGTGCCTCTGACCCAGAGGGAGAAG
ACAATGAGAAAAACAAAAACTGAGCCCTATCGGTCCCCAGCCATGGCTGGGGGGTTGTTTGCCATTGAACGGGATTTCTT
CTTTGAACTGGGTCTCTATGATCCGTGTCTTCAGATCTGGGGTGGTGAAAACTTTGAGATTTCTTACAAAATATGGCAAT
GTGGTGGCAAATTGTTGTTTGTCCTTGTTCTAGAGTTGGACATATCTATCGTCTTGAGGGCTGGCAAGGAAATCCTCCCC
CAATTTATTTAGGATCTTCTCCAACGTTAAAGAACTACATTAGAGTTGTGGAGGTTTGGTGGGATGGCTACAAAGACTAT
TTCTATGCCAGTCGCCCTGAATCAAAAGCACTGCCCTACGGGGATATATCAGAACTGAAAAAATTTCGGGAAGATCACAA
CTGCAAAAGTTTTAAGTGGTTCATGGAAGAAATAGCTTATGATATCATCTCACACTATCCTTTGCCACCCAAGAATGTCG
AGTGGGGAGAGATCAGA

ORF - retro_mdom_1409 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.88 %
Parental protein coverage: 97.46 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMRLKIGFILRSLLVVGSFLGLVVLWSSLSPRPDGQNPLNGMREGRDLNVPIPNRGGNGLAPGGDRFKPVV
MRLKIGFIL.SLLVVGSFLGLVVLWSSLSPRPDGQNPLNGMREGRDLNVPIP.RGGNGLAPGGDRFKPVV
RetrocopyMRLKIGFILCSLLVVGSFLGLVVLWSSLSPRPDGQNPLNGMREGRDLNVPIPIRGGNGLAPGGDRFKPVV
ParentalPWPHVEGVEVDLESIRRKNKAKNEQE-HQAG-GINQQNALQRQYLTFKPQTLTYHDPVLRPGIIGNFEPK
PWPHVEGVEVDLESIRRKNKAKN.QE.H..G..........RQYLT.KPQTLTYHDPVLR.GIIGNFEPK
RetrocopyPWPHVEGVEVDLESIRRKNKAKNKQEHHAGG>STSKMPSRDRQYLTLKPQTLTYHDPVLRLGIIGNFEPK
ParentalEPEPHGVLGGPGEEAKPYVLGPDYKESIHASIKEFGFNMVASDMISLDRSINDLRQEECKYWHYDENLLT
EPEPHGVL.GPGEEAKPYVLGPDYKESIHASIKEFGFN.VASDMISLDRSINDL.QEECKYWHYDENLL.
RetrocopyEPEPHGVLRGPGEEAKPYVLGPDYKESIHASIKEFGFNIVASDMISLDRSINDLQQEECKYWHYDENLLI
ParentalSSVVIVFHNEGWSTLMRTVHSVIKRTPRKYLAEIVLIDDFSNKAHLKERLDEYIKQWNGLVKVFRNERRE
SSVVIVFHNE.WSTLMRTVHS.IKRTPRKYLAEIVLIDDFSNKA.LKERLD.YIKQWN.LVKVFRNERRE
RetrocopySSVVIVFHNERWSTLMRTVHSIIKRTPRKYLAEIVLIDDFSNKALLKERLDDYIKQWNDLVKVFRNERRE
ParentalGLIQARSIGAHKAKLGQVLIYLDAHCEVAVNWYAPLVAPISKDRTTCTVPLIDYIDGNDYSIEPQQGGDE
GLIQARSIGAHKAKLGQVLIYLD.HC.VAVNWYAPLVAPISKDRT..TV..ID.IDGN...I.PQ.GGDE
RetrocopyGLIQARSIGAHKAKLGQVLIYLDVHCDVAVNWYAPLVAPISKDRTVSTVLIIDIIDGNNFKIMPQGGGDE
ParentalDGFARGAWDWSLLWKRIPLSHKEKAKRKHKTEPYRSPAMAGGLFAIERDFFFELGLYDPGLQIWGGENFE
DG..R.AWDWSLL.KR.PL...EK..RK.KTEPYRSPAMAGGLFAIERDFFFELGLYDP.LQIWGGENFE
RetrocopyDGYTRRAWDWSLLRKRVPLTQREKTMRKTKTEPYRSPAMAGGLFAIERDFFFELGLYDPCLQIWGGENFE
ParentalISYKIWQCGGKLLFV-PCSRVGHIYRLEGWQGNPPPIYLGSSPTLKNYIRVVEVWWDGYKDYFYASRPES
ISYKIWQCGGKLLFV.PCSRVGHIYRLEGWQGNPPPIYLGSSPTLKNYIRVVEVWWDGYKDYFYASRPES
RetrocopyISYKIWQCGGKLLFV<PCSRVGHIYRLEGWQGNPPPIYLGSSPTLKNYIRVVEVWWDGYKDYFYASRPES
ParentalKALPYGDISELKKFREDHNCKSFKWFMEEIAYDIISHYPLPPKNVEWGEVR
KALPY..................KWFMEEIAYDIISHYPLPPKNVEWGE.R
RetrocopyKALPYXXXXXXXXXXXXXXXXXXKWFMEEIAYDIISHYPLPPKNVEWGEIR

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_1409 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1409 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000078401 retrocopy
retro_cfam_220,
Monodelphis domestica ENSMODG00000025055 1 retrocopy
retro_mdom_1409 ,
Tupaia belangeri ENSTBEG000000121221 retrocopy
retro_tbel_2374,


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