RetrogeneDB ID:

retro_mdom_1949

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:8:280764726..280765077(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23
Ensembl ID:ENSMODG00000012634
Aliases:None
Description:ribosomal protein L23 [Source:HGNC Symbol;Acc:10316]


Retrocopy-Parental alignment summary:






>retro_mdom_1949
CTGGGTTTCCTAATGTGTGTAGTCATCAGTTGGCCTGATAATGCAAGTGCCAAGAACCTGTGCATCATCTCTGTGAATGG
GGATTAAAGGAAAACTGAGCAGGCTTCCTGAAGCTGGTGTGGGTGACCTCCTAAGGACCACAGTCAAAAAGGGAAACCAG
AGTTCCAAAAAAGGTTCATCCAGCAATGATAATTTGGTCACAGAAATCATAGCAGAGAAAGAAGGAGTGTTTCTATATTT
TGAAGACAATGCAGAGGTCATAGTAAATAACAAAGGCAAGATGAAAAGTTTAGCCATTATGGAGCTGGTTGCCAACAAGT
GGCCAGGACTTCATCTAATGCCAGCAACATT

ORF - retro_mdom_1949 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.84 %
Parental protein coverage: 87.14 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLGLPVGAVINCADNTGAKNLYIISVKG-IKGRLNRLPAAGVGDMVMATVKKG-KPELRK-KVHPAVVIRQ
LG.....VI...DN..AKNL.IISV.G.IKG.L.RLP.AGVGD....TVKKG.KPE..K.KVHPA..I..
RetrocopyLGFLMCVVISWPDNASAKNLCIISVNG>IKGKLSRLPEAGVGDLLRTTVKKG<KPEFQK<KVHPAMIIWS
ParentalRKSYRRK-DGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP-RIASNAGSI
.KS..RK..GVFLYFEDNA.VIVNNKG.MK..AI...VA......WP.R..SNA..I
RetrocopyQKS*QRK<EGVFLYFEDNAEVIVNNKGKMKSLAIMELVANK----WP<RTSSNASNI

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_1949 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1949 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 12 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000042686 retrocopies
Callithrix jacchus ENSCJAG000000083119 retrocopies
Gorilla gorilla ENSGGOG000000250829 retrocopies
Latimeria chalumnae ENSLACG000000044301 retrocopy
Macaca mulatta ENSMMUG000000045029 retrocopies
Monodelphis domestica ENSMODG00000012634 3 retrocopies
retro_mdom_1949 , retro_mdom_527, retro_mdom_916,
Mustela putorius furoENSMPUG000000150752 retrocopies
Nomascus leucogenys ENSNLEG000000006427 retrocopies
Oryctolagus cuniculus ENSOCUG000000139156 retrocopies
Otolemur garnettii ENSOGAG000000124457 retrocopies
Ochotona princeps ENSOPRG0000000195710 retrocopies
Rattus norvegicus ENSRNOG0000000410710 retrocopies



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