RetrogeneDB ID:

retro_mdom_1341

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:69578913..69579393(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000007136
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mdom_1341
GAACCTACTGTGAGCTTTTGTGACCAGAATCAGAGTACTGATGGTGTTAGCCGAAGGTCCATAAAGTACTGCAACTTCTT
TGTCTTTGCCAAATTTTCAATGGACACCTTTGTTAGGTTTAACAGTGTTTCCATTAACACACTGAAGATTGGGAGCCAAC
ATTTGCTTGGTGTTACCCAAATCTGAAATCTGTGAATGACTTGATTTACAAACAAGTTCACGGCAAGATAAATAGACAGA
AAATTACCCTGACTGATAATGCCCTTGTTGAAGAATCTCTTGGTAAAAATGGAATTATCTGCATGGAAGATTTGATCCAT
GAGAATTATACTGTCGATGAGCACTTCAAAGCTGCTGACAACTTACTGTGGCCCTTCAAATTGTTTTCTTCCTAAGGTGG
AATGAAGGAAAAAATCTATACATTTTGTGGGAGGTAAAAATGCTGGTAACAAGGAAGACCAGGTCAATAGACTTGGAAGA

ORF - retro_mdom_1341 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.46 %
Parental protein coverage: 62.02 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalEPKLAFVIRIRGINGVS-PKVRKVLQLLRLRQIFNG-TFVKLNKASINMLRI-VEPYIAWGYPNLKSVND
EP...F........GVS.PKV.KVLQLL.L.QIFNG.TFV..N..SIN.L.I..EP..AW.YPNLKSVND
RetrocopyEPTVSFCDQNQSTDGVS<PKVHKVLQLLCLCQIFNG>TFVRFNSVSINTLKI<WEPTFAWCYPNLKSVND
ParentalLIYKRGYGKIKKQRIALTDNALIAKSLGKYGIICMEDLIHEIYTVGKHFKAANNFLWPFKLSSPRGGMK-
LIYK...GKI..Q.I.LTDNAL...SLGK.GIICMEDLIHE.YTV..HFKAA.N.LWPFKL.S..GGMK.
RetrocopyLIYKQVHGKINRQKITLTDNALVEESLGKNGIICMEDLIHENYTVDEHFKAADNLLWPFKLFSS*GGMK>
ParentalKKTTHFVEGGDAGNREDQINRLIR
KK..HFV.G..AGN.EDQ.NRL.R
RetrocopyKKSIHFVGGKNAGNKEDQVNRLGR

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_1341 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1341 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 33 parental genes, and 423 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000018215 retrocopies
Bos taurus ENSBTAG0000002013922 retrocopies
Canis familiaris ENSCAFG0000000802128 retrocopies
Callithrix jacchus ENSCJAG000000076861 retrocopy
Cavia porcellus ENSCPOG0000000414018 retrocopies
Dasypus novemcinctus ENSDNOG0000001765415 retrocopies
Equus caballus ENSECAG000000091881 retrocopy
Erinaceus europaeus ENSEEUG000000103073 retrocopies
Echinops telfairi ENSETEG0000000565633 retrocopies
Felis catus ENSFCAG000000284466 retrocopies
Homo sapiens ENSG0000014760449 retrocopies
Latimeria chalumnae ENSLACG000000035711 retrocopy
Loxodonta africana ENSLAFG0000001711010 retrocopies
Macropus eugenii ENSMEUG000000163199 retrocopies
Microcebus murinus ENSMICG000000028808 retrocopies
Myotis lucifugus ENSMLUG000000285503 retrocopies
Macaca mulatta ENSMMUG000000051411 retrocopy
Monodelphis domestica ENSMODG00000007136 4 retrocopies
Monodelphis domestica ENSMODG000000190281 retrocopy
Mustela putorius furoENSMPUG0000001024015 retrocopies
Mus musculus ENSMUSG0000004371615 retrocopies
Nomascus leucogenys ENSNLEG000000266158 retrocopies
Oryctolagus cuniculus ENSOCUG0000000840712 retrocopies
Otolemur garnettii ENSOGAG000000039032 retrocopies
Pongo abelii ENSPPYG0000001867150 retrocopies
Pteropus vampyrus ENSPVAG0000000929210 retrocopies
Rattus norvegicus ENSRNOG0000000699227 retrocopies
Sorex araneus ENSSARG000000010883 retrocopies
Sus scrofa ENSSSCG000000061823 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000458618 retrocopies
Tupaia belangeri ENSTBEG000000023011 retrocopy
Tarsius syrichta ENSTSYG0000000610025 retrocopies
Tursiops truncatus ENSTTRG0000000907416 retrocopies



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