RetrogeneDB ID:

retro_mdom_2023

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:X:55698396..55698786(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000003877
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000019421
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_2023
AAGTTATATGATGGCTTTGATGAAGAATACGAATGTCCCATTTTGGATGAAGACAGAGTAGTTGATGAGTTAGAAAATAA
AATGAAAGAAGGTGGAGTTATCGTTGATTACCATGGCTGTGACTTCTTCCCCGAACGATGGTTTCATATAGTTTTTGTAC
TTCAAACAGATAATTCTGTATTATATACAAGACTTGAAAAGAGGGGATACAGTGTAAAGAAACTACAGGACAATGTTCAG
TGTGAAATTTTCCAAATTCTTTATGAAGAAGCCATGACCTCCTACAAGCCTGAAATAGTACACCGGCTGCCCAGCAATGT
ACCAGAAGAACTAGAGAGTAATTTAGATCAGATAATTAAATGGATTGAGGAGTGGATAAAAGAGAATAAT

ORF - retro_mdom_2023 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.15 %
Parental protein coverage: 76.02 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQLYDGFDEEYVCPILDEDRVVDELENKMKEGGVIVDYHGCDFFPERWFHIVFVLQTDNSVLYTRLEKRGY
.LYDGFDEEY.CPILDEDRVVDELENKMKEGGVIVDYHGCDFFPERWFHIVFVLQTDNSVLYTRLEKRGY
RetrocopyKLYDGFDEEYECPILDEDRVVDELENKMKEGGVIVDYHGCDFFPERWFHIVFVLQTDNSVLYTRLEKRGY
ParentalSIKKLQDNVQCEIFQILYEEAMASYKPEIVHRLPSNVPEELESNLDQIIKWIEEWIKDNN
S.KKLQDNVQCEIFQILYEEAM.SYKPEIVHRLPSNVPEELESNLDQIIKWIEEWIK.NN
RetrocopySVKKLQDNVQCEIFQILYEEAMTSYKPEIVHRLPSNVPEELESNLDQIIKWIEEWIKENN

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_2023 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_2023 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 17 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000124714 retrocopies
Callithrix jacchus ENSCJAG000000364211 retrocopy
Dasypus novemcinctus ENSDNOG000000245243 retrocopies
Gorilla gorilla ENSGGOG000000155451 retrocopy
Macropus eugenii ENSMEUG0000001602212 retrocopies
Myotis lucifugus ENSMLUG000000289324 retrocopies
Monodelphis domestica ENSMODG00000019421 14 retrocopies
Mustela putorius furoENSMPUG000000145881 retrocopy
Mus musculus ENSMUSG000000789412 retrocopies
Nomascus leucogenys ENSNLEG000000040862 retrocopies
Oryctolagus cuniculus ENSOCUG000000209701 retrocopy
Otolemur garnettii ENSOGAG000000277364 retrocopies
Pongo abelii ENSPPYG000000155273 retrocopies
Pan troglodytes ENSPTRG0000001694910 retrocopies
Rattus norvegicus ENSRNOG000000398481 retrocopy
Sarcophilus harrisii ENSSHAG000000172162 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000244482 retrocopies



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