RetrogeneDB ID:

retro_itri_1615

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393575.1:442322..442753(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CDC42
Ensembl ID:ENSSTOG00000000805
Aliases:None
Description:cell division cycle 42 [Source:HGNC Symbol;Acc:1736]


Retrocopy-Parental alignment summary:






>retro_itri_1615
ATGCAGACAATTAAGTGTGTTGTTGTAGGCAACGGTACTGTTGGTAAAACACTCCTCCTGATAGCCTACACAACAAGCAA
ATCTCCATCTGAATCTGTATCGTTTGTTTTTGACAACTATGCAGTCACAATTTTGATTGGTGGGAGAGCCATACACTCTT
GGACTTTTTGATACCACAGGGCAAGAGGATTATGACAGATTACAGCTGCTGAGTTAACCACAAACAGATGTATCTCCTGA
TCTGTTTTTCAGTGGTCTCTCTCTCTCCATCCTTATTTGAAAATGTGAAAGAAAAGTGGGTCCCTGAAATAACTCACCCA
CTGGCCCCCAAAACTTTTTTCTTGTTCATTGGGACCCAAATTAATCTCAGAGATAACCCCTCTACTCTTGAGTAACTTGC
CAAGAACAAAGAAAAGTCTATCACTCCAGAG

ORF - retro_itri_1615 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.55 %
Parental protein coverage: 73.3 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIG-GEPYTLGLFDTAGQEDYDRLRP
MQTIKCVVVG.G.VGKT.LLI.YTT.K.PSE.V..VFDNYAVT..IG.GEPYTLGLFDT.GQEDYDRL..
RetrocopyMQTIKCVVVGNGTVGKTLLLIAYTTSKSPSESVSFVFDNYAVTILIG>GEPYTLGLFDTTGQEDYDRLQL
ParentalLSYPQTDV-FLVCFSVV--SPSSFENVKEKWVPEITHH-CPKTPFLLVGTQIDLRDDPSTIEKLAKNKQK
LS.PQTDV..L.CFSVV..SPS.FENVKEKWVPEITH...PKT.FL..GTQI.LRD.PST.E.LAKNK.K
RetrocopyLS*PQTDV>LLICFSVVSLSPSLFENVKEKWVPEITHPLAPKTFFLFIGTQINLRDNPSTLE*LAKNKEK
ParentalPITPE
.ITPE
RetrocopySITPE

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






Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_1615 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1615 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 25 parental genes, and 93 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000147075 retrocopies
Choloepus hoffmanni ENSCHOG0000000530610 retrocopies
Callithrix jacchus ENSCJAG000000059126 retrocopies
Cavia porcellus ENSCPOG000000065434 retrocopies
Dipodomys ordii ENSDORG000000103743 retrocopies
Equus caballus ENSECAG000000191801 retrocopy
Echinops telfairi ENSETEG000000044431 retrocopy
Felis catus ENSFCAG000000048534 retrocopies
Gorilla gorilla ENSGGOG000000244395 retrocopies
Macaca mulatta ENSMMUG000000220098 retrocopies
Monodelphis domestica ENSMODG000000160783 retrocopies
Mustela putorius furoENSMPUG000000159992 retrocopies
Mus musculus ENSMUSG000000066993 retrocopies
Nomascus leucogenys ENSNLEG000000081984 retrocopies
Oryctolagus cuniculus ENSOCUG000000099861 retrocopy
Otolemur garnettii ENSOGAG000000142611 retrocopy
Pongo abelii ENSPPYG000000017556 retrocopies
Rattus norvegicus ENSRNOG000000135361 retrocopy
Sorex araneus ENSSARG000000051843 retrocopies
Ictidomys tridecemlineatus ENSSTOG00000000805 4 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000067841 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000237661 retrocopy
Tarsius syrichta ENSTSYG0000000067911 retrocopies
Tursiops truncatus ENSTTRG000000057082 retrocopies
Vicugna pacos ENSVPAG000000069193 retrocopies



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