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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgttgcaatagtcttgcagaccatattaccatggttagaaatatcacatcgcagtgacattttgcattctgaatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCTAAGAAGGATTGCTTGTGCTTCATAGAGGTGATTGTACACAAGGATGACA

Basic information

species Oryza sativa
transcript LOC_Os01g06660.1
intron # 5
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|88479939|gb|CI417210.1|CI417210
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|87034351|gb|CI188975.1|CI188975
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|86592292|gb|CI250946.1|CI250946
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88490731|gb|CI428003.1|CI428003
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|86413007|gb|CI067412.1|CI067412
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGGCCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|86863055|gb|CI344828.1|CI344828
EST:     GTGTGGT-GAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCCTCAGGGACC
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAG-CTCAGGGACC
EST: gi|88274982|gb|CI395586.1|CI395586
EST:     GTTTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88486081|gb|CI423352.1|CI423352
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88228758|gb|CI228238.1|CI228238
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88280742|gb|CI401940.1|CI401940
EST:     TGGAAGCNTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: TGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|29633272|gb|CB638281.1|CB638281
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|89191318|gb|CI393171.1|CI393171
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTACTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTTAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88473365|gb|CI410636.1|CI410636
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88472167|gb|CI409438.1|CI409438
EST:     GTNTGGTGGAAGCGTTCCATAATGGCGAGGGGAANTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88383762|gb|CI545913.1|CI545913
EST:     TACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: TACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|86845665|gb|CI346983.1|CI346983
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAA-                         GTCCTAACTGAGGAGGAAGCTGAAGGAAGCAATTGAAGAAGGCTCAGGGAC
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAA-CTGAAGGAAGCAATTGAAGAA-GCTCAGGGAC
EST: gi|88284621|gb|CI406067.1|CI406067
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|88483140|gb|CI420411.1|CI420411
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|86496833|gb|CI139466.1|CI139466
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|58689676|gb|CK078363.1|CK078363
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACCGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
EST: gi|86541046|gb|CI181252.1|CI181252
EST:     GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAG                         GTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT
genomic: GTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCT

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: 74 (upstream exon), 70 (downstream exon)
Score: 9

GGAGATCCATGACGGTCCTTACAATGTCATCAAGAATTGGAACTACACCGGTGTGGTGGAAGCGTTCCATAATGGCGAGGGGAAGTGCTACACGGCAAAGgtcagtgttg ... aatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCTAAGAAGGATTGCTTGTGCTTCATAGAGGTGATTGTACACAAGGATGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccatggttagaaatatcacatcgcagtgacattttgcattctgaatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCTAAGAAGGATTGCTTGTGCTTCATAGAGGTGATTGTACACAAGGATGACA
        ttagaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgttgcaatagtcttgcagaccatattaccatggttagaaatatcacatcgcagtgacattttgcattctgaatcttgcagGTCCGAACTGAGGAGGAACTGAAGGAAGCAATTGAAGAAGCTCAGGGACCTAAGAAGGATTGCTTGTGCTTCATAGAGGTGATTGTACACAAGGATGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG