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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgcatatgctcatatgttaagacttcaaatattgttataatccagtagttcattgtttctagttcattagtttatataactaattaccataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTCGCGACGTTTGCGAAGGAACGATATAGCAAGATCCCTCAACCTTGACGGG

Basic information

species Oryza sativa
transcript LOC_Os01g22510.1
intron # 6
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|58586474|gb|CF984782.1|CF984782
EST:     CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTG
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTG
EST: gi|33816970|gb|CF334318.1|CF334318
EST:     CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|15856154|gb|BI808966.1|BI808966
EST:     TGAAATTTT-GCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAA-GGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: TGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|4716419|gb|AU057535.1|AU057535
EST:     GGCACCTGTTGCGTCA                         -NACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: GGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|33676318|gb|CF304557.1|CF304557
EST:     CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|18386325|gb|BM419524.1|BM419524
EST:     CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|88383394|gb|CI540807.1|CI540807
EST:     GCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: GCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|33675987|gb|CF304226.1|CF304226
EST:     CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|4716420|gb|AU057536.1|AU057536
EST:     GCACCTGTTGCGTCA                         GCACTGAANCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: GCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|87025583|gb|CI254629.1|CI254629
EST:     CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|88261028|gb|CI364604.1|CI364604
EST:     ACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: ACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|88427894|gb|CI554402.1|CI554402
EST:     AACTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: AACTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|86852194|gb|CI319129.1|CI319129
EST:     CTGAC-GT-GCTTATGAAGTTCCT-AAATTTT-GCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGGCTGCTTATGCAAGGTTTAGAACGTTT
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAA-GGGCTGCTTATGCAAGGTTTAGAACGTTT
EST: gi|33685901|gb|CF314140.1|CF314140
EST:     CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
EST: gi|33663233|gb|CF294200.1|CF294200
EST:     TGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA                         GCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC
genomic: TGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTC

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: 50 (upstream exon), 74 (downstream exon)
Score: 14

CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCAgtaagttgca ... accataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTCGCGACGTTTGCGAAGGAACGATATAGCAAGATCCCTCAACCTTGACGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccagtagttcattgtttctagttcattagtttatataactaattaccataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTCGCGACGTTTGCGAAGGAACGATATAGCAAGATCCCTCAACCTTGACGGG
                                     aactaat  putative branch site (score: 14)
                   tagttcattagtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgcatatgctcatatgttaagacttcaaatattgttataatccagtagttcattgtttctagttcattagtttatataactaattaccataacagGCACTGAAGCCATTTCTGGAAGGGCTGCTTATGCAAGGTTTAGAACGTTTCGCGACGTTTGCGAAGGAACGATATAGCAAGATCCCTCAACCTTGACGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA