RetrogeneDB ID: | retro_itri_1808 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393851.1:107731..109363(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SPTY2D1 | ||
| Ensembl ID: | ENSSTOG00000009291 | ||
| Aliases: | None | ||
| Description: | SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:26818] |
Retrocopy-Parental alignment summary:
>retro_itri_1808
AATCAAGCAGAGTCAGAGCAGGAGTATGAGGAAGAGCAAGTACCTCCCAAAGTTGAAAGCAAACCAAAGGTTCCCCTTAA
AAGTGCTCCACCACCTATGAACTCCACAGATTTACTGAGGCTGGCTGAGAAAAAGCAGTTTGAACCAGTGGAGATCAAGG
TAGTGAAGAAATCAGAAGAGCAGCTTATGACTGCAGAAGAACTTAGGGAGTGAGAATTCTGGAATGAAAGCATAGGAAAA
AGAAACTTGAGACAGATGCAAAACTACCTCCAACTGTGTCCAAAAAGGCACCCTCTCAGAAAGAAAGTGTGGGCACACAA
CTTAGCAAATGTTCTGGGGAGAAGCATCCTTCCTGTAAAGGAATGTCCTTCCTCATACTGAGAAGAAATCCGAACCCACT
ACAGCCCATGAGAAACACTTATCAGTCTTCATCCAAATCCATGCCAGGAGAGAGGACCAAGGCAGGACCTGGCTGTAGTT
CCCAGCCCTCACTTTGTGAGGGTCATGACAGACCTGTTTTCAATGGGGCTATAAAGCCCCACTCTTGCACCTATTCACCA
AGTGTCCCAAAGACTCCTGCCAGTGGGACTCAGAAATCTGCTACTGAGCACAAAGCCAAAAAATTTCCTCCTTTTCATCC
TAGCCATTCCGAGCCTGGGCCCACAGTCACCCCCACACAATAAGGCTAAGAGTCCAGGTGCCAGGCAGCTAGGCAGCAAC
TCCCAACTCAGTCCCTGGGAGACCCAGCCCAGGGACTGCTCAGTCCATACTTAATTCTGGCCTTGTGCCTAGATGCCAGA
ATGGGAGCTCCAGCTCAGGACCTGAGCGCTGGGTCAGTGGGATCAGGAAGCTGGTCAGTGACTCAAATCCTTCTGGGGGA
ACAGTAACTGATACAAATGACCCTGAATGACCTGCTAAGTAGTTCAAGTGGCCTGGGTGACCCATCAGTGTCTCAGGTAG
TTCTGGGAGACTTGTGGGCAGCTCTGGAGGCCCCAGGCAGCCCACAAGCAGTCCACATGACCTTTGACAACTGGTGACTG
GCTCAGGACCCCTTGGATGATCCGTCAGTGGGCTTGGACGATTCATAAGGGGCTCCATTCCAGCTGGACACACTAGTTCA
GGCCCTGGAAGACCCGTAAGTGGCTTAGGACCTGGGTGAACAGTTAGTAGCCCAGGTCCCCTTTAAAGCCCAAGTGTAAT
GTTGTCTCAGAAATAGTATCTTCCAAGAATAGTATTAGTGGAGCCTGCAACGGACAGGTAAACGGAATGAAACCTTCTCT
CTCTGGCTACAGCTCTGCCCGAGCTCCTCAAAGACTTCCTTTCCCTACTGGTTGTAAAAGGCAGTGAGGATATGAGGAGG
AAGATGATGATGATGATGAATATGACTCTGAACTGGATAATTTCATTGAAGATGAAGGAGAACCTTAGGAAGAATTATCC
AAGCATATTCTAGAAATCTTTGGCTATGACTGAAAAAAACACAAAGATGAAAGTGATTATGCCTTATGTTACATGGAGAG
TAGTTGGAATGAAGAAGCAGAGTTTAAGACTAGGTATTCAGGAGGACATAGAGGAAATGAGACGTGAAGAAGAAGAAATG
AAATGTAGAAAAGCAAAGAAGCTGAAGAGATT
ORF - retro_itri_1808 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.56 % |
| Parental protein coverage: | 80.12 % |
| Number of stop codons detected: | 13 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | NQAESEQEYEEEQVPPKVESKPKVPLKSAPPPMNFTDLLRLAEKKQFEPVEIKVVKKSEERPMTAEELRE |
| NQAESEQEYEEEQVPPKVESKPKVPLKSAPPPMN.TDLLRLAEKKQFEPVEIKVVKKSEE..MTAEELRE | |
| Retrocopy | NQAESEQEYEEEQVPPKVESKPKVPLKSAPPPMNSTDLLRLAEKKQFEPVEIKVVKKSEEQLMTAEELRE |
| Parental | REF-LERKHRKKKLETDAKLPPTVSKKAPSQKESVGTKLSKGSGDRRLSSKGMPF-PHSEKKSKPSTAHE |
| .EF.LE.KHRKKKLETDAKLPPTVSKKAPSQKESVGT.LSK.SG....S.KGM.F.PH.EKKS.P.TAHE | |
| Retrocopy | *EF<LE*KHRKKKLETDAKLPPTVSKKAPSQKESVGTQLSKCSGEKHPSCKGMSF<PHTEKKSEPTTAHE |
| Parental | KHLSV-SSSKSMPGERTKAGSGCSSQPSLREGHDRPVFNGAGKPHSSTYSPSVPKTSASGTQKSATEHKA |
| KHLSV.SS.KSMPGERTKAG.GCSSQPSL.EGHDRPVFNGA.KPHS.TYSPSVPKT.ASGTQKSATEHKA | |
| Retrocopy | KHLSV>SS-KSMPGERTKAGPGCSSQPSLCEGHDRPVFNGAIKPHSCTYSPSVPKTPASGTQKSATEHKA |
| Parental | KKFPPFHPSHSKPGPTVT-PHNKAKSPGTRQPGSNS-NSAPGRPSPGTARSILSSGPVPRRQNGSSSSGP |
| KKFPPFHPSHS.PGPTVT.PHNKAKSPG.RQ.GSNS.NS.PGRPSPGTA.SIL.SG.VPR.QNGSSSSGP | |
| Retrocopy | KKFPPFHPSHSEPGPTVT>PHNKAKSPGARQLGSNS>NSVPGRPSPGTAQSILNSGLVPRCQNGSSSSGP |
| Parental | EHSASGTKKLVSDSNPSGPTVTGTNGPGRPATISSGPGRPINVSGSSGRLVGSSGGPGRPTSSPHDLRQP |
| E...SG..KLVSDSNPSG.TVT.TN.P..PA.....PG.PI.VSGSSGRLVGSSGGP..PTSSPHDL.Q. | |
| Retrocopy | ERWVSGIRKLVSDSNPSGGTVTDTNDPE*PAK*FKWPG*PISVSGSSGRLVGSSGGPRQPTSSPHDL*QL |
| Parental | VTSSGPPGRSVSGLGRSISGSVPAGRIISSSGPGRPVSGLGPGRTVSSPGP-PLKPKCTVVSETISSKNI |
| VT.SGP.G.SVSGLGR.I.GS.PAG....SSGPGRPVSGLGPG.TVSSPGP.PLKPKC.VVSE..SSKN. | |
| Retrocopy | VTGSGPLG*SVSGLGRFIRGSIPAGH--TSSGPGRPVSGLGPG*TVSSPGP<PLKPKCNVVSEIVSSKNS |
| Parental | ISRTSNGQINGMKPALSGYRSAQGPQRLPFPTSYKRQRGYEEE-DDDDEYDSEMDDFIEDEGEPQEEISK |
| IS...NGQ.NGMKP.LSGY.SA..PQRLPFPT..KRQ.GYEEE.DDDDEYDSE.D.FIEDEGEP.EE.SK | |
| Retrocopy | ISGACNGQVNGMKPSLSGYSSARAPQRLPFPTGCKRQ*GYEEEDDDDDEYDSELDNFIEDEGEP*EELSK |
| Parental | HIREIFGYDRKKYKDESDYALRYMESSWKEQQKEEAKSLRLGMQEDLEEMRREEEEMKRRKAKKL |
| HI.EIFGYD.KK.KDESDYAL.YMESSW.E....E.K....G.....E..RR..E..K...A... | |
| Retrocopy | HILEIFGYD*KKHKDESDYALCYMESSWNEE--AEFKTRYSGGHRGNET*RRRNEM*KSKEAEEI |
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_1808 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1808 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 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000009291 | 1 retrocopy |
retro_itri_1808 ,
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