RetrogeneDB ID:

retro_itri_1855

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH394176.1:4874..5310(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000015375
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_1855
GTCAGTTTTGTATTAATATTAAAAAATGAGCACTTCACCACTGCTTCATCTCTGAAGTCTCAGAGCCGCCTTTTCTGCTT
TCCTGAGTTCTAGTGGAGGGATAACAGGAAGCGAGAGCGATGATTCTGATGAATGTTCAGTTGTGGGAGTCGGGATGAAT
TGCCTGCGAGTGCTTCTGGCGTACAACAGAGAAAATGCCAGAAGACGCCCAACAAGCTAGCAAGGGAAGAAAATGCTCCA
AAGGGAGGGCCAGAAGCAGTTTACTCAGAACAGACTCAGAGACAATTGTACCTCCTGGGAAAAGCAAGTACTTGTGGAAA
GCAAAATAAGAAGGCATGAGGACCCAGGAAGGAAAGAGTGAGTTATCTGGAGCCACAGGATGCTGATAAGGAAGTGTCTC
CAGGCATAGGAAGAGACCAGCAGCCCTGAGGAAGAA

ORF - retro_itri_1855 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.39 %
Parental protein coverage: 75.79 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalITYVYLKRN--YTTMTSL-GLRATLPAFMSSNRQIIESQSDDSDECR-NRGSQDELPKSASGIRQRKRKE
...V....N...TT..SL..LRA...AF.SS...I..S.SDDSDEC....GS.DELP.SASG..QRK...
RetrocopyVSFVLILKNEHFTTASSL>SLRAAFSAFLSSSGGITGSESDDSDECS<SCGSRDELPASASGVQQRKC-Q
ParentalKMPKKPAMEENDPKGVPKAVGSEQAQRQLYPLGKASTSGKQSEKVSGPRKKNVN-IWSHRLRERKYLVAY
K.P.K.A.EEN.PKG.P.AV.SEQ.QRQLY.LGKAST.GKQ..K..GPRK..V..IWSHR...RK.L.A.
RetrocopyKTPNKLAREENAPKGGPEAVYSEQTQRQLYLLGKASTCGKQNKKA*GPRKERVS>IWSHRMLIRKCLQA*
ParentalEEISDPEEE
EE.S.PEEE
RetrocopyEETSSPEEE

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_1855 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1855 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 8 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000147761 retrocopy
Homo sapiens ENSG000002046451 retrocopy
Gorilla gorilla ENSGGOG000000261071 retrocopy
Macaca mulatta ENSMMUG000000191641 retrocopy
Nomascus leucogenys ENSNLEG000000035041 retrocopy
Pongo abelii ENSPPYG000000203651 retrocopy
Pan troglodytes ENSPTRG000000218571 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000015375 3 retrocopies
retro_itri_1394, retro_itri_1855 , retro_itri_746,



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