RetrogeneDB ID:

retro_itri_663

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393309.1:3776688..3777031(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL9
Ensembl ID:ENSSTOG00000002077
Aliases:None
Description:ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]


Retrocopy-Parental alignment summary:






>retro_itri_663
GTATATAACATAATCAAAGGTGTTACACTGGGCTCTATTACAGGATAAGGTCTATGTATGCTCACTGCCCCTTCAGTGCA
TTATTCAGGAGAGTGGGGCTCCTGTTTAAATCTGAAATTTCCTGGGTGAATACACCTGCAGGGTTCAGATGAGGCCAGGT
ATTGCTTATTCAGTTTCTCAAACCCAGAAAAATGAGTTGATCCTTGAAAGAAATGACATGGAACTTGTTTCAAATTCAGC
TGCTTTGAATCAGCAAGCCACAACATGTAAAAACAAGGACATTACAAAATTTTGAGATGTGATCTATATCTCTGAAAAAA
GAACAGTTCAGTAGATTGATGAA

ORF - retro_itri_663 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.95 %
Parental protein coverage: 60.42 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVQNMIKGVTLG-FRYKMRSVYAH-FPINVVIQENGSLVEIRNFLGEKYIRRVRMRTGVACSVSQAQKDEL
V.N.IKGVTLG...Y..RS.YAH..P....IQE.G..V.I.NFLGE.Y..RV.MR.G.A.SVSQ.QK.EL
RetrocopyVYNIIKGVTLG<LYYRIRSMYAH<LPLQCIIQESGAPV*I*NFLGE-YTCRVQMRPGIAYSVSQTQKNEL
ParentalILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIYVSEKGTVQQADE
ILE.ND.ELVSNSAAL.QQATT.KNKDI.KF.D.IY.SEK.TVQ..DE
RetrocopyILERNDMELVSNSAALNQQATTCKNKDITKF*DVIYISEKRTVQ*IDE

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_663 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_663 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 15 parental genes, and 176 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
Cavia porcellus ENSCPOG0000000454315 retrocopies
Danio rerio ENSDARG000000373501 retrocopy
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
Dipodomys ordii ENSDORG000000010886 retrocopies
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
Gadus morhua ENSGMOG000000010021 retrocopy
Macropus eugenii ENSMEUG000000167228 retrocopies
Myotis lucifugus ENSMLUG0000000459734 retrocopies
Monodelphis domestica ENSMODG000000205537 retrocopies
Mus musculus ENSMUSG000000472152 retrocopies
Otolemur garnettii ENSOGAG0000000493520 retrocopies
Rattus norvegicus ENSRNOG000000267163 retrocopies
Sarcophilus harrisii ENSSHAG000000049188 retrocopies
Ictidomys tridecemlineatus ENSSTOG00000002077 13 retrocopies



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