RetrogeneDB ID:

retro_mdom_1938

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:8:203505317..203505771(-)
Located in intron of:ENSMODG00000029640
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NANOG
Ensembl ID:ENSMODG00000017979
Aliases:None
Description:Nanog homeobox [Source:HGNC Symbol;Acc:20857]


Retrocopy-Parental alignment summary:






>retro_mdom_1938
CCTAAGCAGATCCGAAATGTGGCTGAGAATTTGAACCTTACTTACAAATAGGTCAAGCCCTGGTTTTAGAACCAGAGAAT
GAAATCAAAGAGATGGCAGAAAGATACCACGTAGTCAAAGAATGGCAACCGTAATGTTCAGAATGGATCAGCTCTTGGGG
AGTATATAAGTCTCTACTCTCCATTTCACTAGGACTATATGGTTAGTTCTTCTGGAACCCTTCCAGTATGGAGCAACCAG
ACTTGGAATAATCAGTTCCAGAATAGTGATGAGGGCTCCTATCAGCATTAGATATTTCAGCACTCTTACCCTGCCAGTGA
CTTGGGGACTACCTTTGGAAGTAATACTAGTGGGGCTTATCCCATCAAAATCACAGACTTCTATGAGTTTTAGTACCCTC
TACCCCATGGAATATCTCCCAAGCTACTCCATGAACATGCAACTGACCCACAGC

ORF - retro_mdom_1938 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.5 %
Parental protein coverage: 53.93 %
Number of stop codons detected: 5
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPQQIRNVAENLNLTYKQVKTWFQNQRMKSKRWQKDTMWTKNGNRNVQNGSALGEYISLYSPFHQDYMVSS
P.QIRNVAENLNLTYK.VK.WF.NQRMKSKRWQKDT...KNGNRNVQNGSALGEYISLYSPFH.DYMVSS
RetrocopyPKQIRNVAENLNLTYK*VKPWF*NQRMKSKRWQKDTT*SKNGNRNVQNGSALGEYISLYSPFH*DYMVSS
ParentalSGTLPVWSNQTWNNQFQNSGEGSYQHQIFQHSYPASDLGATFGNNTGGAYSM-KSQTSLSFNTPYPMEYL
SGTLPVWSNQTWNNQFQNS.EGSYQH.IFQHSYPASDLG.TFG.NT.GAY...KSQTS.SF.T.YPMEYL
RetrocopySGTLPVWSNQTWNNQFQNSDEGSYQH*IFQHSYPASDLGTTFGSNTSGAYPI>KSQTSMSFSTLYPMEYL
ParentalPSYSMNMQLTHS
PSYSMNMQLTHS
RetrocopyPSYSMNMQLTHS

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_1938 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1938 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 23 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000170641 retrocopy
Canis familiaris ENSCAFG000000139141 retrocopy
Choloepus hoffmanni ENSCHOG000000009724 retrocopies
Callithrix jacchus ENSCJAG000000189998 retrocopies
Cavia porcellus ENSCPOG000000026211 retrocopy
Echinops telfairi ENSETEG000000046488 retrocopies
Felis catus ENSFCAG000000016211 retrocopy
Homo sapiens ENSG000001117045 retrocopies
Gorilla gorilla ENSGGOG000000281964 retrocopies
Macropus eugenii ENSMEUG000000099492 retrocopies
Microcebus murinus ENSMICG000000022281 retrocopy
Myotis lucifugus ENSMLUG000000293252 retrocopies
Myotis lucifugus ENSMLUG000000305801 retrocopy
Macaca mulatta ENSMMUG000000321584 retrocopies
Monodelphis domestica ENSMODG00000017979 2 retrocopies
retro_mdom_1293, retro_mdom_1938 ,
Mustela putorius furoENSMPUG000000167315 retrocopies
Nomascus leucogenys ENSNLEG000000053593 retrocopies
Oryctolagus cuniculus ENSOCUG000000137831 retrocopy
Otolemur garnettii ENSOGAG000000263391 retrocopy
Procavia capensis ENSPCAG000000154602 retrocopies
Pongo abelii ENSPPYG000000042335 retrocopies
Pan troglodytes ENSPTRG000000298074 retrocopies
Pteropus vampyrus ENSPVAG000000069891 retrocopy



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