RetrogeneDB ID:

retro_mdom_1397

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:278836078..278836489(-)
Located in intron of:ENSMODG00000004859
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000010312
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1397
ATGGATGATAGCAACCATGATTCCCAGTTTGAGCCCATTTTCTCTGCCTGAACAGGAGATTAAGACCTTGGAGGAAGATG
AAGAAGAGCTCTTTAAGATGCGAGATAAGCTGTTCTGATTTGCATCTGAGAATGACCTTCCAGAGTGGAAAGAGCGAGGG
ACAGGTGATGTGAAGCTACTGAAACACAAGGAGAAAGGGACAATTCACCTCCTCATGAGGTGGGACAAGACTCTCAAGAT
CTGTGTGAATCACTGTATAACCCCCCGATGGAGCTAAAGCCCAATTCAGGCAGTGACAGGGCTTAGGTTTGGAACACACA
TGTTGACTTTGCCAATGAAAGTACAAAGCCAGAGCTGCTGGCCATCTGATTCCTGAATGCAGAAAATGCCCAGAAGTTTA
AGGCAAAATTC

ORF - retro_mdom_1397 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.71 %
Parental protein coverage: 70.77 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMDDSNHD-PQFEPIVSLPEQEIKTLEEDEEELFKMRAKLFRFASENDLPEWKERGTGDVKLLKHKEKGTI
MDDSNHD.P...P..SLPEQEIKTLEEDEEELFKMR.KLF.FASENDLPEWKERGTGDVKLLKHKEKGTI
RetrocopyMDDSNHD>PSLSPF-SLPEQEIKTLEEDEEELFKMRDKLF*FASENDLPEWKERGTGDVKLLKHKEKGTI
ParentalRLLMRRDKTLKICANHYITPL-MELKPNAGSDRAWVWNTHADFADESPKPELLAIRFLNAENAQKFKAKF
.LLMR.DKTLKIC.NH.ITP..MELKPN.GSDRA.VWNTH.DFA.ES.KPELLAI.FLNAENAQKFKAKF
RetrocopyHLLMRWDKTLKICVNHCITPR<MELKPNSGSDRA*VWNTHVDFANESTKPELLAI*FLNAENAQKFKAKF

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_1397 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1397 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 19 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000107491 retrocopy
Cavia porcellus ENSCPOG000000029621 retrocopy
Dipodomys ordii ENSDORG000000113172 retrocopies
Echinops telfairi ENSETEG000000159962 retrocopies
Homo sapiens ENSG000000999012 retrocopies
Gorilla gorilla ENSGGOG000000007841 retrocopy
Macropus eugenii ENSMEUG000000166208 retrocopies
Myotis lucifugus ENSMLUG000000175351 retrocopy
Macaca mulatta ENSMMUG000000201001 retrocopy
Monodelphis domestica ENSMODG00000010312 5 retrocopies
Mus musculus ENSMUSG000000057321 retrocopy
Nomascus leucogenys ENSNLEG000000056842 retrocopies
Otolemur garnettii ENSOGAG000000343332 retrocopies
Pongo abelii ENSPPYG000000115934 retrocopies
Rattus norvegicus ENSRNOG000000018844 retrocopies
Sarcophilus harrisii ENSSHAG000000068731 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000268402 retrocopies
Tarsius syrichta ENSTSYG000000135731 retrocopy
Tursiops truncatus ENSTTRG000000081422 retrocopies



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