RetrogeneDB ID:

retro_dord_283

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:GeneScaffold_82:85328..85687(+)
Located in intron of:ENSDORG00000005649
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:H3f3b
Ensembl ID:ENSDORG00000008132
Aliases:None
Description:H3 histone, family 3B [Source:MGI Symbol;Acc:MGI:1101768]


Retrocopy-Parental alignment summary:






>retro_dord_283
CCCAGGAAACAACTGGCAACAAAGCTACTCACAAGAGTACAGCCTCTCCTAGAAGGGTGGAGAGACCTTATCATTAAAGG
CCTAGTACAGTGGCACTTTGTGAAATTAGACACTACCAGAAGTCCACTGAACTTCTGATATGCAAGCTCCCTATCCACTG
TCTGGTGCGAGAAATTGCTCAGGACTTCAAAACAGATCTGTGCTTCCAGAACCCAGCGATTGGTGCTTTACAGGAGGCAA
GTGAGGCCTATCTGGTTGGCCTTTTTGAAGTTACCAATCTATGTGCTATACATGGCAAATGGATAACAATTATGCCAAAA
GATATCCAGCTAGCATACCACATAGATGGAGAAAGTGCT

ORF - retro_dord_283 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.38 %
Parental protein coverage: 88.24 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPRKQLATK-AARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRF
PRKQLATK.A..KS..S...V..P...RP.TVAL.EIR.YQKSTELLI.KLP...LVREIAQDFKTDL.F
RetrocopyPRKQLATK<ATHKSTASPRRVERPYH*RPSTVALCEIRHYQKSTELLICKLPIHCLVREIAQDFKTDLCF
ParentalQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Q..AIGALQEASEAYLVGLFE.TNLCAIH.K..TIMPKDIQLA..I.GE.A
RetrocopyQNPAIGALQEASEAYLVGLFEVTNLCAIHGKWITIMPKDIQLAYHIDGESA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Dipodomys ordii was not studied using RNA-Seq expression data.
Dipodomys ordii was not studied using ChIP-Seq data.
Dipodomys ordii was not studied using EST data.
Dipodomys ordii was not studied using FANTOM5 data.
retro_dord_283 was not experimentally validated.

Retrocopy orthology:
Dipodomys ordii 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 115 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000245613 retrocopies
Canis familiaris ENSCAFG000000049162 retrocopies
Canis familiaris ENSCAFG000000161194 retrocopies
Dipodomys ordii ENSDORG00000008132 9 retrocopies
Erinaceus europaeus ENSEEUG000000137961 retrocopy
Felis catus ENSFCAG000000036174 retrocopies
Felis catus ENSFCAG000000304245 retrocopies
Gorilla gorilla ENSGGOG0000002252611 retrocopies
Gadus morhua ENSGMOG000000143061 retrocopy
Macaca mulatta ENSMMUG000000314839 retrocopies
Mus musculus ENSMUSG0000001655918 retrocopies
Nomascus leucogenys ENSNLEG000000015772 retrocopies
Otolemur garnettii ENSOGAG0000002431211 retrocopies
Otolemur garnettii ENSOGAG0000002593314 retrocopies
Pongo abelii ENSPPYG0000000016814 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Pteropus vampyrus ENSPVAG000000084592 retrocopies
Rattus norvegicus ENSRNOG000000032204 retrocopies



Copyright © RetrogeneDB 2014-2017