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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcagacttaacagctggttatattgtattgttctgcctctgcatgtgttacgtagccatttaacttctggagactaaaattttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGACTAGAAAAGTTTGGCTGAGCATGGGAGTAGCACCGAAGCAGATTCAAGGT

Basic information

species Oryza sativa
transcript LOC_Os08g37960.2
intron # 7
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88906936|gb|CI376008.1|CI376008
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88251342|gb|CI349770.1|CI349770
EST:     ACCATCACCACAGCGTGGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: ACCATCACCACAGCGT-GCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88381193|gb|CI525963.1|CI525963
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|86414166|gb|CI068569.1|CI068569
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88303599|gb|CI508205.1|CI508205
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88460369|gb|CI529444.1|CI529444
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88287585|gb|CI507475.1|CI507475
EST:     TGCTGGCTCCCGTAGGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: TGCTGGCTCCCGTA-GCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88271227|gb|CI387280.1|CI387280
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAATCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|86832469|gb|CI344719.1|CI344719
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88462064|gb|CI504562.1|CI504562
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88466511|gb|CI532318.1|CI532318
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88562919|gb|CI493636.1|CI493636
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|55411089|gb|CV723465.1|CV723465
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|58685259|gb|CK073946.1|CK073946
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88419085|gb|CI511237.1|CI511237
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88264124|gb|CI367898.1|CI367898
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|18388196|gb|BM421394.1|BM421394
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAA-TTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88318450|gb|CI505854.1|CI505854
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88379273|gb|CI508791.1|CI508791
EST:     ACCATCACCACGGCGTGCTGGCTCCC-TAGGCCCAGGTAGTGATGACAAG                         GAATAAANTTTGTTGATCCAGTGATGGTTAAGAAGAGTCTTCAAATTGGAC
genomic: ACCATCACCACAGCGTGCTGGCTCCCGTA-GCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88564601|gb|CI495318.1|CI495318
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTATTGATGACAAG                         GAATAAANTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88568160|gb|CI498877.1|CI498877
EST:     ACCATCACCACAGCGTGCTGGCTCCC-TAGCNNCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: ACCATCACCACAGCGTGCTGGCTCCCGTAGC-CCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88318037|gb|CI501008.1|CI501008
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88567387|gb|CI498104.1|CI498104
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88378226|gb|CI503792.1|CI503792
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88461532|gb|CI504659.1|CI504659
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|86426964|gb|CI072061.1|CI072061
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88446945|gb|CI528988.1|CI528988
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88464884|gb|CI512189.1|CI512189
EST:     CACCATCACCACGGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAATCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|15856504|gb|BI809316.1|BI809316
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88437633|gb|CI511534.1|CI511534
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88846771|gb|CI373539.1|CI373539
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88565299|gb|CI496016.1|CI496016
EST:     CACCATCACCACAGCGTGGTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88293019|gb|CI507797.1|CI507797
EST:     CACCATCACCACAGCGTGCTGGCTCCCTTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|86538521|gb|CI178727.1|CI178727
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCTAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88468299|gb|CI512314.1|CI512314
EST:     CACCATCACCACAGCGTGGTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|88562902|gb|CI493619.1|CI493619
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
EST: gi|87033116|gb|CI187740.1|CI187740
EST:     CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAG                         GAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC
genomic: CACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 68 (upstream exon), 75 (downstream exon)
Score: 27

TCCTGAAAAAGAGACAAATGGAAAAGGTTCACCTCCTTCACGCAGTGTTTCACCATCACCACAGCGTGCTGGCTCCCGTAGCCCAGGTAGTGATGACAAGgtaagtttca ... tttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGACTAGAAAAGTTTGGCTGAGCATGGGAGTAGCACCGAAGCAGATTCAAGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctgcatgtgttacgtagccatttaacttctggagactaaaattttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGACTAGAAAAGTTTGGCTGAGCATGGGAGTAGCACCGAAGCAGATTCAAGGT
                                    gactaaa  putative branch site (score: 27)
                                            ttttctttc  CT-rich tract
                                     actaaaattttcttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcagacttaacagctggttatattgtattgttctgcctctgcatgtgttacgtagccatttaacttctggagactaaaattttctttcagGAATAAAGTTTGTTGATCCAGTGATGCTTAAGAAGAGTCTTCAAATTGGACTAGAAAAGTTTGGCTGAGCATGGGAGTAGCACCGAAGCAGATTCAAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT