RetrogeneDB ID:

retro_opri_934

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_4732:128091..129072(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC35A1
Ensembl ID:ENSOPRG00000019035
Aliases:None
Description:solute carrier family 35 (CMP-sialic acid transporter), member A1 [Source:HGNC Symbol;Acc:11021]


Retrocopy-Parental alignment summary:






>retro_opri_934
AATGTCAGTTTACTATTCAAGTTATACTGCTTGACAGTGACGCCTCTGGTGGCCGCAGCGTACACCATAGCTCTAGGGCA
TACAGGAACAACAAATACAGAGCGCTACTCTTCAACCGCAGCGGTGTGTAGGACAGAAGTTGTAAAGTCACTGCTAAGTG
TGGGACTTTTAGCTGAAGAAACTGGTAGTCTGGGTAGATTCAAGACATCTTTATGTGAAAATGTTTTTGGGAGTCCCAAG
CAACTGATGAAGTTAAGTGTGCCGTCACTAGTGCATGCTGTTCAGAACAACATGGCTCTCCTAGCCCTTAGCAATCTGGA
TGCAGCAGTGTGCCAGGTGACCTACCAACTGAAGACTCCCTGTACTGCTTTATGTACTGTTTTAATGTTAAATAGGACAC
TCAGTAAATTATAGTGGATTTCAGTTTTTATGCTGTGTGGCGGAGTCACACTTGTACAGTGGAAACCAGCCCAAGCTACA
AAAGTTGTGGTGGAGCAGACTCCATTACTAGGGTTTGGCGCCATAGCTGTTGCTGTTCTGTGCTCAGGATTTGCTGGAGT
GTATTTTGAAAAAGTTTTAAAGAGTTCAGACACTTCCCTTGGGGTGAGAAACATTCAAATGTATCTATCAGGGATTGCTG
AGGCATTAGTTGGTGTCTACTTGTCAGACGGAGCTGAAATTAAAGAAAAAGGATTTTTCTATGGTTACACACATTATGTC
TGGTTTGTTATCTTTCTGGCAAGTGTTGGAGGCCTTTACACCTCGGTGGTGGACAAGCACACCGACAACATCATGAAAGG
GTTTTCCATTGTGCTTTCCACCATTGCTTCAGCGATCCTGTTTGGATTACAGATAACACTTACCTTTACTTTGGGCACCC
TTCTTGTATGTGTTTCCATTTATATCTATGGACAACCCAGGCAAGACACTACATCCATCCAACAAGGAGAAACAGCTTCG
AAAGAAAAAATCATTGGTGTG

ORF - retro_opri_934 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.33 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNVSLLFKLYCLTVMTLVAAAYTIALRYTRTTSTERYFSTTAVCITEVVKLLLSVGLLAKETGSLGRFKTS
NVSLLFKLYCLTV..LVAAAYTIAL..T.TT.TERY.ST.AVC.TEVVK.LLSVGLLA.ETGSLGRFKTS
RetrocopyNVSLLFKLYCLTVTPLVAAAYTIALGHTGTTNTERYSSTAAVCRTEVVKSLLSVGLLAEETGSLGRFKTS
ParentalLCENVFGSPKELMKLSVPSLVYAVQNNMAFLALSNLDAAVYQVTYQLKIPCTALCTVLMLNRTLSKLQWI
LCENVFGSPK.LMKLSVPSLV.AVQNNMA.LALSNLDAAV.QVTYQLK.PCTALCTVLMLNRTLSKL.WI
RetrocopyLCENVFGSPKQLMKLSVPSLVHAVQNNMALLALSNLDAAVCQVTYQLKTPCTALCTVLMLNRTLSKL*WI
ParentalSVFMLCGGVTLVQWKPAQATKVVAEQNPLLGFGAIAVAGLCSGFAGVYFEKVLKSSDTSLWVRNIQMYLS
SVFMLCGGVTLVQWKPAQATKVV.EQ.PLLGFGAIAVA.LCSGFAGVYFEKVLKSSDTSL.VRNIQMYLS
RetrocopySVFMLCGGVTLVQWKPAQATKVVVEQTPLLGFGAIAVAVLCSGFAGVYFEKVLKSSDTSLGVRNIQMYLS
ParentalGIAVTLVGVYLSDGAEIKEKGFFYGYTHYVWFVIFLASVGGLYTSVVVKYTDNIMKGFSAAAAIVLSTIA
GIA..LVGVYLSDGAEIKEKGFFYGYTHYVWFVIFLASVGGLYTSVV.K.TDNIMKGFS....IVLSTIA
RetrocopyGIAEALVGVYLSDGAEIKEKGFFYGYTHYVWFVIFLASVGGLYTSVVDKHTDNIMKGFS----IVLSTIA
ParentalSVILFGLQITLTFTLGALLVCVSIYIYGLPRQDTTSIQQGETASKEKIIGV
S.ILFGLQITLTFTLG.LLVCVSIYIYG.PRQDTTSIQQGETASKEKIIGV
RetrocopySAILFGLQITLTFTLGTLLVCVSIYIYGQPRQDTTSIQQGETASKEKIIGV

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






Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_934 was not experimentally validated.

Retrocopy orthology:
Ochotona princeps 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 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Ochotona princeps ENSOPRG00000019035 2 retrocopies
retro_opri_35, retro_opri_934 ,
Pan troglodytes ENSPTRG000000184051 retrocopy



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