RetrogeneDB ID:

retro_mdom_1132

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:3:199529472..199529731(-)
Located in intron of:ENSMODG00000010821
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:H3F3A
Ensembl ID:ENSMODG00000005983
Aliases:None
Description:H3 histone, family 3A [Source:HGNC Symbol;Acc:4764]


Retrocopy-Parental alignment summary:






>retro_mdom_1132
AGTAAAACTTCTAGGAAAAGTGCCCTCTCTACCAGGGAGGTCATGAAACCTCAAGCTTGGCATCCTGGGACTTTAGCACT
TCCTGAGATTCATCATTACCAGAACTCAACAGAGTTTTTGATCAAGAAAACTCTATTTCCAGCAGCTTCCAAGGGAGATT
GTCCAGGACTTCAAAGTACACTTGAAGTTGCAAAATGGTACTACTGGTATCCGCCAGGAGGCAAGTGAAGCATATTTAAT
AGTTTTCTTTGAAGACTCA

ORF - retro_mdom_1132 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.62 %
Parental protein coverage: 63.24 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLI-RKLPFQRLVREIAQDFKTDLRFQSAAIG
.K..RKSA.ST..V.KP....PGT.AL.EI..YQ.STE.LI.RKL.FQ.L.REI.QDFK..L..Q....G
RetrocopySKTSRKSALSTREVMKPQAWHPGTLALPEIHHYQNSTEFLI>RKLYFQQLPREIVQDFKVHLKLQNGTTG
ParentalALQEASEAYLVGLFEDT
..QEASEAYL...FED.
RetrocopyIRQEASEAYLIVFFEDS

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_1132 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1132 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 18 parental genes, and 99 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000145887 retrocopies
Bos taurus ENSBTAG000000245613 retrocopies
Canis familiaris ENSCAFG000000049162 retrocopies
Canis familiaris ENSCAFG000000161194 retrocopies
Erinaceus europaeus ENSEEUG000000137961 retrocopy
Felis catus ENSFCAG000000036174 retrocopies
Felis catus ENSFCAG000000304245 retrocopies
Gadus morhua ENSGMOG000000143061 retrocopy
Macaca mulatta ENSMMUG000000314839 retrocopies
Monodelphis domestica ENSMODG00000005983 3 retrocopies
retro_mdom_1037, retro_mdom_1132 , retro_mdom_175,
Mustela putorius furoENSMPUG000000138113 retrocopies
Nomascus leucogenys ENSNLEG000000015772 retrocopies
Otolemur garnettii ENSOGAG0000002431211 retrocopies
Otolemur garnettii ENSOGAG0000002593314 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Pan troglodytes ENSPTRG0000000204520 retrocopies
Pteropus vampyrus ENSPVAG000000084592 retrocopies
Tursiops truncatus ENSTTRG000000158897 retrocopies



Copyright © RetrogeneDB 2014-2017