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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcaggagcacacttgctttcttggctaatatttttcatccccttgttcctttttcatacgtgtcttcttgtgtgatcatattgatttactcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG

Basic information

species Oryza sativa
transcript LOC_Os07g39630.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 5
gtgcaggagcacacttgctttcttggctaatatttttcatccccttgttcctttttcatacgtgtcttcttgtgtgatcatattgatttactcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG
                      |||  | || ||||| |  |    || | |||   |||  |||  ||| || || |||||||    ||||  || ||||||||  |||||||||||||||| |||||||| |||||||| || || |||||||| |||
-----------------gcaagttgcttcat-tttttaactcataagtacttttcatatat-tgtggtctagtctggtcatattatgctactataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG
















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|29675062|gb|CB671337.1|CB671337
EST:     TTTGACATTGCATCAGATGCTTCTGCGGCCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: TTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|29673566|gb|CB669841.1|CB669841
EST:     CTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: CTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|29673647|gb|CB669922.1|CB669922
EST:     CTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: CTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|58695257|gb|CK083944.1|CK083944
EST:     TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCCGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCAACCGTGGCAGAATTTCTGTCGAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|29664684|gb|CB660959.1|CB660959
EST:     TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|58663168|gb|CK051854.1|CK051854
EST:     TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|29656023|gb|CB652298.1|CB652298
EST:     TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|66915714|gb|CX102562.1|CX102562
EST:     TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCCGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCAACCGTGGCAGAATTTCTGTCGAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|58688748|gb|CK077435.1|CK077435
EST:     T-CAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|29660229|gb|CB656504.1|CB656504
EST:     TACAACTTCCAAATTTTGACATTGCATCAAATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|58674983|gb|CK063670.1|CK063670
EST:     TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT
EST: gi|29629034|gb|CB634045.1|CB634045
EST:     TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCCGCGACCTTTAAG                         GAACTTCTGACAAGGCATAAAGCAACCGTGGCAGAATTTCTGTCGAAGAAT
genomic: TACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAAT

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: 72 (upstream exon), 60 (downstream exon)
Score: 99

GTACGTTTTAGAGTCTGACCACATGAAGAAGTTCTTTGACTATATACAACTTCCAAATTTTGACATTGCATCAGATGCTTCTGCGACCTTTAAGgtgatttgct ... ctcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcctttttcatacgtgtcttcttgtgtgatcatattgatttactcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG
                                   tattgat  putative branch site (score: 99)
                                         tttactc  CT-rich tract
                               atcatattgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcaggagcacacttgctttcttggctaatatttttcatccccttgttcctttttcatacgtgtcttcttgtgtgatcatattgatttactcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
gtgcagg
- - - -agcacac
- - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcttg