RetrogeneDB ID:

retro_mdom_674

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:65822342..65822888(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL13
Ensembl ID:ENSMODG00000003663
Aliases:None
Description:ribosomal protein L13 [Source:HGNC Symbol;Acc:10303]


Retrocopy-Parental alignment summary:






>retro_mdom_674
GCTCCAAGCAGCCATAGCACCACATTGAAATGGCACAATTCTGACTGGCAAAGACAAGTTGTCTCATGGTTTAACAAGCC
AGTCGGAAAGATCCAAAGACAAAAGGCCCATCAAGCAAAAGCCTGTTGAATTGCTTCTCTCCCTGCATCTGGTCCTATCT
GGCCAGTAGTGAGGTACCCTACTGCGATTCCACACCAAGTGCCTGCTAGTAGAGGATTCAGCTTGGAAGAGCTTCTAATG
GCTGATATCTATAAAAAAGTGGCATGTACTATTAGGATCTTTGTGGACCTTTGCCACTGAAATACTTCCAAAGAAACTCT
ACAGAGAAATATTCAGTCATTGAAAGAATATCGTTCCAAATTAATCCTCTTCCCAAGGAAACCATTGACTCCTAAGAAGG
GAAATAGTTCTCCTGAAGAATTCAAGTTGCCAACCTAGCTTTCAGCACCAGTTATACCCATCAGAAATGTTTACAAGAAA
GAAAAAACTCATGTTATTACTGAAAATGAGAAGCATCTCATGGTCTTTGCGCACCTTCAAATGGCA

ORF - retro_mdom_674 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.04 %
Parental protein coverage: 87.2 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRCPTVRYHTKVR
APS.....LK.H...DWQR.V..WFN.P..KI.R.KA.QAKA..IA..PASGPI.P.VR.PT...H..V.
RetrocopyAPSSHSTTLKWH-NSDWQRQVVSWFNKPVGKIQRQKAHQAKAC*IASLPASGPIWPVVRYPTAIPH-QVP
ParentalAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSA
A.RGFSLEEL..A.I.KKVA.TI.I.VD....N.S.E.LQ.N.Q.LKEYRSKLILFPRKP..PKKG.SS.
RetrocopyASRGFSLEELLMADIYKKVACTIRIFVDLCH*NTSKETLQRNIQSLKEYRSKLILFPRKPLTPKKGNSSP
ParentalEELKLATQLSGPVMPIRNVFKKEKARVITEDEKNFKAFASLRMA
EE.KL.T.LS.PV.PIRNV.KKEK..VITE.EK....FA.L.MA
RetrocopyEEFKLPT*LSAPVIPIRNVYKKEKTHVITENEKHLMVFAHLQMA

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_674 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_674 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 24 parental genes, and 153 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000170721 retrocopy
Ailuropoda melanoleuca ENSAMEG000000011115 retrocopies
Bos taurus ENSBTAG000000120442 retrocopies
Canis familiaris ENSCAFG000000198405 retrocopies
Callithrix jacchus ENSCJAG000000096725 retrocopies
Cavia porcellus ENSCPOG000000273484 retrocopies
Echinops telfairi ENSETEG000000150574 retrocopies
Felis catus ENSFCAG000000033384 retrocopies
Homo sapiens ENSG0000016752612 retrocopies
Gorilla gorilla ENSGGOG000000254276 retrocopies
Loxodonta africana ENSLAFG000000040545 retrocopies
Microcebus murinus ENSMICG000000081914 retrocopies
Myotis lucifugus ENSMLUG000000109506 retrocopies
Macaca mulatta ENSMMUG000000179287 retrocopies
Monodelphis domestica ENSMODG00000003663 4 retrocopies
Mus musculus ENSMUSG0000000074023 retrocopies
Nomascus leucogenys ENSNLEG0000001577413 retrocopies
Ornithorhynchus anatinus ENSOANG000000067291 retrocopy
Otolemur garnettii ENSOGAG000000264443 retrocopies
Pan troglodytes ENSPTRG0000000848012 retrocopies
Pteropus vampyrus ENSPVAG000000151306 retrocopies
Rattus norvegicus ENSRNOG0000001533514 retrocopies
Sus scrofa ENSSSCG000000249743 retrocopies
Vicugna pacos ENSVPAG000000005694 retrocopies



Copyright © RetrogeneDB 2014-2017