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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaatcaaccaatggctatattagatggttgatctctggaaggcatatgagcagatatacgctgtgatcttaagtgttgactcccaatttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAAGCCTTTACTAATCTTAATTCTGGTGAGTTGCTCCTCCGTAGCAGAGCTC

Basic information

species Oryza sativa
transcript LOC_Os04g55940.1
intron # 11
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|88381904|gb|CI530710.1|CI530710
EST:     TTATGTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|86484481|gb|CI127114.1|CI127114
EST:     TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|88906701|gb|CI375773.1|CI375773
EST:     TTATCTAATATTTGCCGCCACTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|88504390|gb|CI431896.1|CI431896
EST:     TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|88254126|gb|CI352752.1|CI352752
EST:     TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|88262940|gb|CI366566.1|CI366566
EST:     TTATCTAATA-TTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|88384803|gb|CI556681.1|CI556681
EST:     AGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: AGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|66923908|gb|CX110756.1|CX110756
EST:     TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACC
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACC
EST: gi|86832984|gb|CI333583.1|CI333583
EST:     TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|86258579|gb|CI064932.1|CI064932
EST:     TTATCTAATAGTTGCCGCCAGTTTCCTCGTCCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|33381504|gb|CF196847.1|CF196847
EST:     TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|88321436|gb|CI535388.1|CI535388
EST:     CTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: CTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|86863308|gb|CI344966.1|CI344966
EST:     TTATCTAATAG-TGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
EST: gi|58669001|gb|CK057687.1|CK057687
EST:     TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCA                         GCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA
genomic: TTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAA

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: 63 (upstream exon), 65 (downstream exon)
Score: 8

GATGGTGTTGCGAACTACTTGAAAGGACTTATGCTGATCTTGTGTTATCTAATAGTTGCCGCCAGTTTCTTCGTTCACGTTGATCCACAATCCAgtaagtagag ... ttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAAGCCTTTACTAATCTTAATTCTGGTGAGTTGCTCCTCCGTAGCAGAGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatgagcagatatacgctgtgatcttaagtgttgactcccaatttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAAGCCTTTACTAATCTTAATTCTGGTGAGTTGCTCCTCCGTAGCAGAGCTC
                               tgttgac  putative branch site (score: 8)
                                     ctcccaattttttt  CT-rich tract
                                          aattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaatcaaccaatggctatattagatggttgatctctggaaggcatatgagcagatatacgctgtgatcttaagtgttgactcccaatttttttgcagGCGATGATTGATGCCACGGACACTGTAATTATTGTACCAAATACCCTTGAAGCCTTTACTAATCTTAATTCTGGTGAGTTGCTCCTCCGTAGCAGAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - -caaccaa
- - - - - - - - - - - - - atggttg
- - - - - - - - - - - - - - - - - - - - - - gcatatg