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:
| Parental | HFKGVWNIVNNIPFLRNSIMRYVLTSRSHLIDSPPTYNVHYGYKNWEAFSNLSYYTRALPPVADDCPTPM |
| .FKGVWNIVNNIPFL.NSIMRYVLT.RSHLIDSPPTYNVHYGYKNWEAFSNLSYYTRALPPVADDCPTPM | |
| Retrocopy | YFKGVWNIVNNIPFL*NSIMRYVLTFRSHLIDSPPTYNVHYGYKNWEAFSNLSYYTRALPPVADDCPTPM |
| Parental | GVKGKKELPDSKEVFEKVLLRRKFIPDPQGTNMMFAFFAQHFTHQFFKSDRNRGPAFTTGLGHGVDLSHV |
| GVKGKKEL.DSKEVFE.VLLRRKF.PDPQGTNMMFAFFAQHFTHQ..KSDRN.GPAFTTGLGH...LSHV | |
| Retrocopy | GVKGKKELSDSKEVFENVLLRRKFLPDPQGTNMMFAFFAQHFTHQILKSDRNPGPAFTTGLGHRLYLSHV |
| Parental | YGETLDRQHKLRLFKDGKLKYQVIDGEVYPPTVKDTQVEMLYPPHVPEHLQFAVGQEVFGLVPGLMMYAT |
| YGETLDRQHKLRLFKD.KLKYQVIDGEVYPP.VKDTQVEM.YPPHVPEHLQFAVGQ.VFGLVPGLMMYAT | |
| Retrocopy | YGETLDRQHKLRLFKDRKLKYQVIDGEVYPPIVKDTQVEMIYPPHVPEHLQFAVGQKVFGLVPGLMMYAT |
| Parental | IWLREHNRVCDVLKQEHPEWDDERLFQTTRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNQQFQY |
| IWL.EHNRVCDVLKQEHPEWDDE.LFQT.RLILIGETIKIVIEDYVQHL.GYHFKLKFDPELLFNQQFQY | |
| Retrocopy | IWLQEHNRVCDVLKQEHPEWDDEWLFQTSRLILIGETIKIVIEDYVQHLNGYHFKLKFDPELLFNQQFQY |
| Parental | QNRIASEFNTLYHWHPLLPDTFQIHDQEYNYQQFIYNNSILLEHGLTQFVESFSRQIAGRVSGGRNVPSA |
| QN.I.SEFNTLYHWHPLLPDTFQIHDQEYNYQQFIYNNSILL.HGLTQFVE.F.RQIAG.V.GGRNVPS. | |
| Retrocopy | QNHISSEFNTLYHWHPLLPDTFQIHDQEYNYQQFIYNNSILLKHGLTQFVE*FTRQIAGSVFGGRNVPSP |
| Parental | VQAVAKASIDHSRNMKYQSFNEYRKRFNLKPYKSFEELTGEKEMAAELEALYGDIDAVEFYPALLVEKPR |
| VQAVAKASIDHSRNMKYQ.FN.Y.K.FNLKPYK.FEELTGEKEMAAELEALY.DIDA.EFYPA.LVEKPR | |
| Retrocopy | VQAVAKASIDHSRNMKYQCFNDYHKCFNLKPYKLFEELTGEKEMAAELEALYCDIDALEFYPAFLVEKPR |
| Parental | PDAIFGETMVEMGAPFSLKG-LLGNPICSPHYWKPSTFGGEVGFKIINTASIQSLICRNVKGCPFVSFSV |
| PDAIF.ETMVEMGAPFS.K..LLGNP.CSPHYWKPSTFGGE.GFKIINTASIQSLICRNVKGCPFV.FSV | |
| Retrocopy | PDAIFNETMVEMGAPFSFKD<LLGNPMCSPHYWKPSTFGGEEGFKIINTASIQSLICRNVKGCPFV*FSV |
| Parental | QDPLLTKTVTINASASHSRLEDINPTVLLKGRATEL |
| QDPLLTKTVTINAS.SHSRLEDIN.TVLLKG..TEL | |
| Retrocopy | QDPLLTKTVTINASTSHSRLEDINSTVLLKGHSTEL |
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_1651 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
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 ,
|