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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgacgaataatcagaagttcttagtttcttttgaaccttagactgggtttgaaacttaacattatgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAAGCCATCCTTCTCTCCGCCACCGAGGCGGCTGAGATGATTCTCAGGGTTG

Basic information

species Oryza sativa
transcript LOC_Os03g42220.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 18
gtaagttgacgaataatcagaagttcttagtttcttttga--accttagactgggtttgaaacttaacat----tatgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAAGCCATCCTTCTCTCCGCCACCGAGGCGGCTGAGATGATTCTCAGGGTTG
||||||| || ||  |  ||| |||   | | |      |  | |||  || |  | | | |||   ||     | || || ||||||||| ||||||||||||| ||| ||    ||| | |||||||||||||| ||||| ||||| || || || ||||| || |||||||| |||||||| |
gtaagttcacaaa-gacaagatgtttccattcttaacaaattatcttttacagaatctaatactagtcaaattgtgtggtccgcagGTTGGGGACATGCAAAAGCTAGGGATTCAAGAGTCGTTCAAGGTGAAGCAGGCCATTCTTCTGTCTGCAACAGAGGCTGCCGAGATGATCCTCAGGGTCG
















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|86484583|gb|CI127216.1|CI127216
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|86545840|gb|CI186046.1|CI186046
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|58609353|gb|CK037386.1|CK037386
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|86428658|gb|CI075339.1|CI075339
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|89163713|gb|CI100603.1|CI100603
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTGGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88833808|gb|CI077289.1|CI077289
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88547077|gb|CI477349.1|CI477349
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|86867958|gb|CI342809.1|CI342809
EST:     CTGGAATCGATGTCATCACAGGCAGC                         CTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: CTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|38478291|gb|CF962424.1|CF962424
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88959990|gb|CI381868.1|CI381868
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88199291|gb|CI199141.1|CI199141
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88842969|gb|CI371869.1|CI371869
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|29676854|gb|CB673129.1|CB673129
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|89179994|gb|CI044273.1|CI044273
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88272062|gb|CI388115.1|CI388115
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88264494|gb|CI368268.1|CI368268
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88382459|gb|CI535667.1|CI535667
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|29657047|gb|CB653322.1|CB653322
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88288899|gb|CI518030.1|CI518030
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|218484326|gb|FG955561.1|FG955561
EST:     AACACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGG
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGG
EST: gi|88551392|gb|CI481446.1|CI481446
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|89169532|gb|CI109891.1|CI109891
EST:     AGCACCACAAGGAGAGTTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|29616346|gb|CB621358.1|CB621358
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88289083|gb|CI520413.1|CI520413
EST:     CTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: CTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88962004|gb|CI097157.1|CI097157
EST:     ATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: ATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|86823862|gb|CI258850.1|CI258850
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88996823|gb|CI389489.1|CI389489
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88828956|gb|CI073826.1|CI073826
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|86428290|gb|CI074971.1|CI074971
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
EST: gi|88255784|gb|CI353655.1|CI353655
EST:     AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGACATCACAGGCAGC                         GTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA
genomic: AGCACCACAAGGAGAATTGCACTGCTGGAATCGATGTCATCACAGGCAGCgtaagttgac ... tgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttagtttcttttgaaccttagactgggtttgaaacttaacattatgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAAGCCATCCTTCTCTCCGCCACCGAGGCGGCTGAGATGATTCTCAGGGTTG
                                  acttaac  putative branch site (score: 3)
                                aaacttaacattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgacgaataatcagaagttcttagtttcttttgaaccttagactgggtttgaaacttaacattatgatctgcagGTTGGAGACATGCAAAAGCGAGGCATATCGGAGGCCTTCAAGGTGAAGCAAGCCATCCTTCTCTCCGCCACCGAGGCGGCTGAGATGATTCTCAGGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG