RetrogeneDB ID:

retro_mdom_1234

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:38358372..38359174(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MANEA
Ensembl ID:ENSMODG00000018142
Aliases:None
Description:mannosidase, endo-alpha [Source:HGNC Symbol;Acc:21072]


Retrocopy-Parental alignment summary:






>retro_mdom_1234
CTGTCCTGGTACCCATGTGGTTTAGCTGATAATGAAGAGGAATCTACTGATGAGTTGGTGCCTGTATTTTGGATAATGCT
CATAAATATAATCTAAAAGTCACTTTCACATTGAACCATATAAAAGTCAAAATGATCACAGTATGTACAAAATTATCAAG
AACATTATAGATAAATATGGAAGCCATCCAGCTTTTTACAGGTATAAGACTAAAACTGGCAGAGTCTTGCCCATGTTTTA
TGTATATGATTCCTATTTCACAAAGCTGGAAACCTGGGTCAATCTGTTAACTGCCTCAGGTCCCCTGAGTGTTCATAATA
CTCCCTAGGATAGATTGTTTGTTGCTCTTCTTGTAGAAGAAAGACAAAAACAGGAAATCCAGAGAAGTGGTCTTGATGGC
ATTTATACATACTTTGCCACAAATGGCGTTTCTTATGGCTCATCACATCACAACTGGGCAGGTATAAAAGTCTTTTGTGA
CAGCAACAACTTACTGTTTATCCCAAGTGTGGGACCAGGATACATAGACATCAACATACGACCGTGGAACAACCACAACA
CTTGGAACTGAATCAATGGGAAGTACTTTGAAACTACTTTCAATACTGCGCTTCAGGTGTGACCTGATGCTATTTCTATC
ACTTCTTTTAATGAATTGCATGAAGGGACTCAGATTGAAAAAGCATTTCCTGAGAGAACTAAACTCATAGCTTACTTTGA
TTACCAGCCTCACAAACCAGGTATTTATCTGGAACTTACTCATAAATAGTCAGAAAAATACAATAAGGAAAAAGAGCAGT
GG

ORF - retro_mdom_1234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.56 %
Parental protein coverage: 58.77 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLSWYPRGLADKEGESTDELVP-SILDNAHKYNLKVTF-HIEPYKNRDDHSMHKIIKYIIDKYGSHPAFYR
LSWYP.GLAD.E.ESTDELVP..ILDNAHKYNLKVTF.HIEPYK...DHSM.KIIK.IIDKYGSHPAFYR
RetrocopyLSWYPCGLADNEEESTDELVP<CILDNAHKYNLKVTF<HIEPYKSQNDHSMYKIIKNIIDKYGSHPAFYR
ParentalYKTKTGRVLPMFYVYDSYFTKPETWANLLTASGPLSVRNTPYDGLFIALLVEERHKQEIQRSGFDGIYTY
YKTKTGRVLPMFYVYDSYFTK.ETW.NLLTASGPLSV.NTP.D.LF.ALLVEER.KQEIQRSG.DGIYTY
RetrocopyYKTKTGRVLPMFYVYDSYFTKLETWVNLLTASGPLSVHNTP*DRLFVALLVEERQKQEIQRSGLDGIYTY
ParentalFATNGFSYGSSHHNWAVLKAFCDSNSLLFIPSVGPGYIDINIRPWNNHNTRNRINGKYFETAFSAALQVQ
FATNG.SYGSSHHNWA..K.FCDSN.LLFIPSVGPGYIDINIRPWNNHNT.N.INGKYFET.F..ALQV.
RetrocopyFATNGVSYGSSHHNWAGIKVFCDSNNLLFIPSVGPGYIDINIRPWNNHNTWN*INGKYFETTFNTALQV*
ParentalPDAISITSFNEWHEGTQIEKAVPKRTELTVYLDYQPHKPGIYLELTRKWSEKYNKEKEQW
PDAISITSFNE.HEGTQIEKA.P.RT.L..Y.DYQPHKPGIYLELT.K.SEKYNKEKEQW
RetrocopyPDAISITSFNELHEGTQIEKAFPERTKLIAYFDYQPHKPGIYLELTHK*SEKYNKEKEQW

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_1234 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1234 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 ENSMODG00000018142 1 retrocopy
retro_mdom_1234 ,


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