RetrogeneDB ID:

retro_mdom_1172

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:352370265..352370618(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000007612
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000008452
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1172
TGCCATGCTCTCTTCATTGGCTACTGTATGTACTTTGATCGCAAGAGATGGAGCGACCCTAACTTCAAAAAACAGGCTCT
GAGAACAAAGAAACAGAAGCTTGCTAAAGAGAGAGCTGGCTTTCCAAGTTACCTGACCTTAAAGACACACAAGCTGTTCA
GAAGTTCTTCCTTGAAGAAATACAGCTTGGTGAGGAATTACTAGCTCAAGGTGAACATGAAAAGGGTGTTGACCACTTGA
CAAATGCCATTGCTCTCTGTGGACAGCCACAGCAATTGTTGCAAGTTTTACAGCAAACTCTTCCACCACCAGTGTTCCAG
ATGCTTCTGACTAAGCTGCCTACAATCAGCCAG

ORF - retro_mdom_1172 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.33 %
Parental protein coverage: 84.4 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAG-LSKLPDLKDAEAVQKFFLEEIQLGEELL
C.ALFIGYC.YFDRKR.SDPNFK.....R.KKQKLAKERAG.LSKLPDLKD..AVQKFFLEEIQLGEELL
RetrocopyCHALFIGYCMYFDRKRWSDPNFKKQAL-RTKKQKLAKERAG<LSKLPDLKDTQAVQKFFLEEIQLGEELL
ParentalAQGEYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQ
AQGE.EKGVDHLTNAIA.CGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQ
RetrocopyAQGEHEKGVDHLTNAIALCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQ

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_1172 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1172 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 110 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000005625 retrocopies
Choloepus hoffmanni ENSCHOG000000023837 retrocopies
Callithrix jacchus ENSCJAG000000181273 retrocopies
Erinaceus europaeus ENSEEUG000000002211 retrocopy
Echinops telfairi ENSETEG000000176934 retrocopies
Homo sapiens ENSG000001737265 retrocopies
Gorilla gorilla ENSGGOG000000251845 retrocopies
Loxodonta africana ENSLAFG000000154991 retrocopy
Microcebus murinus ENSMICG000000163253 retrocopies
Myotis lucifugus ENSMLUG000000162181 retrocopy
Macaca mulatta ENSMMUG000000071362 retrocopies
Monodelphis domestica ENSMODG00000008452 6 retrocopies
Mus musculus ENSMUSG0000009390412 retrocopies
Oryctolagus cuniculus ENSOCUG000000214702 retrocopies
Otolemur garnettii ENSOGAG000000326932 retrocopies
Pongo abelii ENSPPYG000000000994 retrocopies
Pan troglodytes ENSPTRG000000021275 retrocopies
Pteropus vampyrus ENSPVAG000000151571 retrocopy
Rattus norvegicus ENSRNOG000000199804 retrocopies
Sarcophilus harrisii ENSSHAG000000158763 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000275643 retrocopies
Tupaia belangeri ENSTBEG0000000382726 retrocopies
Tursiops truncatus ENSTTRG000000022004 retrocopies
Vicugna pacos ENSVPAG000000039801 retrocopy



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