RetrogeneDB ID:

retro_itri_1019

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393359.1:7065827..7066172(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MRPL17
Ensembl ID:ENSSTOG00000003313
Aliases:None
Description:mitochondrial ribosomal protein L17 [Source:HGNC Symbol;Acc:14053]


Retrocopy-Parental alignment summary:






>retro_itri_1019
AGTTGCCTTTCACAAGGGAGCTTATTCTGCTGTCAGGACCTTGGTTCCAAGTTCTACATCCACCTATTGCGGAACTTGCT
AATCAGACTGAGATCACACGAATACACAGAGGCATCATGGCACATCTAGATGAAATGAGAGGGAAATGCCTAGAAGATCA
CTGACTATGGGAAGTTGGGAGACACCAAGGAATGAGCCATGCACATGGTTGACTTCTGACTCACAGAGAAATTGATCCCA
AAGTTATTTCAAGTACTGGCCAATCAGCACCAAGGTCAAAATGGGGGCTACACAAGAATGTTGCAGACCCCAAACTGGAG
TGAGCAGTACTAGGCTAAAATAGCA

ORF - retro_itri_1019 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.71 %
Parental protein coverage: 95.08 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAAISHGRVFRRLGLGPESRIHLLRNLLTGLVRHERIEASW-ARVDEMR-GYAEKLIDYGKLGDTNERAMR
...S.G..F....LG....IHLLRNLL..L..HE..EASW.A..DEMR.G.A.K..DYGKLGDT.E.AM.
RetrocopySCLSQGSLFCCQDLGSKFYIHLLRNLLIRLRSHEYTEASW<AHLDEMR>GNA*KITDYGKLGDTKE*AMH
ParentalMADFWLTEKDLIPKLFQVLAPRFQDQNGGYTRMLQIPNSSQQDRAKMA
M.DF.LTEK.LIPKLFQVLA...Q.QNGGYTRMLQ.PN.S.Q..AK.A
RetrocopyMVDF*LTEK-LIPKLFQVLANQHQGQNGGYTRMLQTPNWSEQY*AKIA

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_1019 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1019 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 7 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000275361 retrocopy
Macropus eugenii ENSMEUG000000135881 retrocopy
Myotis lucifugus ENSMLUG000000011442 retrocopies
Mustela putorius furoENSMPUG000000054491 retrocopy
Rattus norvegicus ENSRNOG000000194971 retrocopy
Sus scrofa ENSSSCG000000246931 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000003313 3 retrocopies
retro_itri_1019 , retro_itri_1156, retro_itri_240,



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