RetrogeneDB ID:

retro_itri_1651

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393609.1:1417844..1419418(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PTGS2
Ensembl ID:ENSSTOG00000009613
Aliases:None
Description:prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) [Source:HGNC Symbol;Acc:9605]


Retrocopy-Parental alignment summary:






>retro_itri_1651
TACTTCAAGGGGGTCTGGAACATTGTCAATAATATTCCCTTCCTGTGAAATTCAATCATGAGATATGTGCTGACTTTCAG
ATCACATTTGATTGACAGTCCACCAACTTACAATGTGCACTATGGCTACAAAAACTGGGAAGCCTTCTCGAACCTCTCCT
ACTATACCAGAGCCCTTCCTCCTGTGGCAGATGACTGCCCAACACCCATGGGTGTGAAAGGGAAGAAGGAGCTTTCTGAT
TCTAAAGAGGTGTTTGAAAATGTTCTTTTAAGAAGAAAGTTCCTTCCTGACCCCCAAGGCACCAATATGATGTTTGCATT
CTTTGCTCAGCACTTCACCCATCAAATTCTTAAGTCAGATCGGAATCCAGGGCCAGCTTTCACCACAGGACTGGGCCATA
GGCTGTACCTAAGTCATGTTTATGGTGAAACTCTGGATAGACAACATAAGCTGCGCCTCTTCAAGGATAGAAAACTAAAA
TATCAGGTGATTGATGGAGAGGTGTATCCTCCCATAGTCAAAGACACTCAGGTGGAGATGATCTACCCTCCTCACGTCCC
TGAACACCTTCAGTTTGCAGTGGGGCAGAAGGTCTTTGGTCTAGTGCCTGGTCTGATGATGTATGCAACAATCTGGCTAC
AGGAACATAATCGAGTGTGCGATGTTCTTAAACAGGAACATCCAGAGTGGGATGATGAGTGGTTGTTCCAGACAAGCAGA
CTAATATTAATAGGGGAGACCATTAAAATTGTGATTGAAGACTATGTTCAGCACTTGAATGGCTATCACTTCAAACTGAA
GTTTGACCCAGAGCTGCTTTTCAACCAACAATTCCAGTACCAAAACCATATTTCTTCTGAGTTTAACACACTTTATCACT
GGCATCCCCTTCTGCCTGACACCTTTCAAATTCATGACCAGGAGTACAACTATCAACAGTTTATATACAACAATTCCATA
TTACTGAAACATGGACTTACCCAGTTCGTTGAGTAATTTACCAGGCAAATTGCTGGCAGTGTTTTTGGTGGCAGAAATGT
GCCATCTCCAGTACAAGCAGTGGCCAAGGCCTCAATTGACCATAGCAGAAATATGAAATACCAGTGTTTCAATGATTACC
ACAAATGCTTCAACCTGAAGCCCTACAAATTATTTGAAGAACTTACAGGAGAGAAGGAAATGGCGGCAGAGTTGGAAGCC
CTCTATTGTGACATTGATGCCTTGGAGTTTTATCCTGCCTTCCTGGTGGAAAAGCCTCGTCCTGATGCTATCTTTAATGA
GACCATGGTGGAAATGGGCGCACCATTCTCCTTTAAAGACTTTTGGGTAATCCTATGTGTTCTCCTCACTATTGGAAACC
AAGCACTTTTGGAGGAGAAGAAGGCTTTAAGATCATTAACACTGCCTCTATTCAGTCCCTCATCTGCCGTAACGTGAAGG
GCTGTCCCTTCGTCTAATTCAGTGTTCAGGATCCACTGCTCACCAAGACAGTCACCATCAATGCAAGTACTTCCCACTCC
AGACTAGAAGACATCAATTCCACAGTACTACTGAAAGGACATTCAACAGAACTG

ORF - retro_itri_1651 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.06 %
Parental protein coverage: 86.92 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalHFKGVWNIVNNIPFLRNSIMRYVLTSRSHLIDSPPTYNVHYGYKNWEAFSNLSYYTRALPPVADDCPTPM
.FKGVWNIVNNIPFL.NSIMRYVLT.RSHLIDSPPTYNVHYGYKNWEAFSNLSYYTRALPPVADDCPTPM
RetrocopyYFKGVWNIVNNIPFL*NSIMRYVLTFRSHLIDSPPTYNVHYGYKNWEAFSNLSYYTRALPPVADDCPTPM
ParentalGVKGKKELPDSKEVFEKVLLRRKFIPDPQGTNMMFAFFAQHFTHQFFKSDRNRGPAFTTGLGHGVDLSHV
GVKGKKEL.DSKEVFE.VLLRRKF.PDPQGTNMMFAFFAQHFTHQ..KSDRN.GPAFTTGLGH...LSHV
RetrocopyGVKGKKELSDSKEVFENVLLRRKFLPDPQGTNMMFAFFAQHFTHQILKSDRNPGPAFTTGLGHRLYLSHV
ParentalYGETLDRQHKLRLFKDGKLKYQVIDGEVYPPTVKDTQVEMLYPPHVPEHLQFAVGQEVFGLVPGLMMYAT
YGETLDRQHKLRLFKD.KLKYQVIDGEVYPP.VKDTQVEM.YPPHVPEHLQFAVGQ.VFGLVPGLMMYAT
RetrocopyYGETLDRQHKLRLFKDRKLKYQVIDGEVYPPIVKDTQVEMIYPPHVPEHLQFAVGQKVFGLVPGLMMYAT
ParentalIWLREHNRVCDVLKQEHPEWDDERLFQTTRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQY
IWL.EHNRVCDVLKQEHPEWDDE.LFQT.RLILIGETIKIVIEDYVQHL.GYHFKLKFDPELLFNQQFQY
RetrocopyIWLQEHNRVCDVLKQEHPEWDDEWLFQTSRLILIGETIKIVIEDYVQHLNGYHFKLKFDPELLFNQQFQY
ParentalQNRIASEFNTLYHWHPLLPDTFQIHDQEYNYQQFIYNNSILLEHGLTQFVESFSRQIAGRVSGGRNVPSA
QN.I.SEFNTLYHWHPLLPDTFQIHDQEYNYQQFIYNNSILL.HGLTQFVE.F.RQIAG.V.GGRNVPS.
RetrocopyQNHISSEFNTLYHWHPLLPDTFQIHDQEYNYQQFIYNNSILLKHGLTQFVE*FTRQIAGSVFGGRNVPSP
ParentalVQAVAKASIDHSRNMKYQSFNEYRKRFNLKPYKSFEELTGEKEMAAELEALYGDIDAVEFYPALLVEKPR
VQAVAKASIDHSRNMKYQ.FN.Y.K.FNLKPYK.FEELTGEKEMAAELEALY.DIDA.EFYPA.LVEKPR
RetrocopyVQAVAKASIDHSRNMKYQCFNDYHKCFNLKPYKLFEELTGEKEMAAELEALYCDIDALEFYPAFLVEKPR
ParentalPDAIFGETMVEMGAPFSLKG-LLGNPICSPHYWKPSTFGGEVGFKIINTASIQSLICRNVKGCPFVSFSV
PDAIF.ETMVEMGAPFS.K..LLGNP.CSPHYWKPSTFGGE.GFKIINTASIQSLICRNVKGCPFV.FSV
RetrocopyPDAIFNETMVEMGAPFSFKD<LLGNPMCSPHYWKPSTFGGEEGFKIINTASIQSLICRNVKGCPFV*FSV
ParentalQDPLLTKTVTINASASHSRLEDINPTVLLKGRATEL
QDPLLTKTVTINAS.SHSRLEDIN.TVLLKG..TEL
RetrocopyQDPLLTKTVTINASTSHSRLEDINSTVLLKGHSTEL

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1651 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1651 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 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Ictidomys tridecemlineatus ENSSTOG00000009613 2 retrocopies
retro_itri_1417, retro_itri_1651 ,


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