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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcataatcaaatcaaaggcgacactggagtttgcttgttttcttccatcactctatgttctaaccatctgttttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTAGTTG

Basic information

species Oryza sativa
transcript LOC_Os02g51410.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G161566_T01 (Zea mays), 3'ss of exon 2
--------------------gtactgcataatcaaatcaaaggcgacactggagtttgcttgttttcttccatcactcta-tgttctaaccatctgttttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTAGTTG
                    || ||  |  |||| ||||| |   ||  ||||| |||| ||| || ||  | || |||| |||| |     | |  | |  |||||||||||||||||||||||||| ||||| || || ||  ||||||||||| |||| |
gtattgaccaagatcttggagtcctaaaagatcagatcaatgattactatggagattgcatgtgtttttgtaccagtctaatgttat-----tgtactatgatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTAAACGGGAGGTGTATTTACTTAGTGG

upper sequence: LOC_Os02g51410.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G070218_T01 (Zea mays), 3'ss of exon 2
-----------------------gtactgcataatcaaatcaaaggcgacactggagtttgcttgttttcttccatcactcta-tgttctaaccatctgttttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTAGTTG
                        || | |    ||| |||||      |  |||||  ||| ||| || ||  | |   |||  ||| |     | |  |||  |||||||||||||||||||||||||| ||||| ||||| ||  |||||||||||||||| |
gtattgaccaagatcttgggttcctaatactagctcacatcaataattgctatggagagtgcatgtgtttttgtaccggcctaacgttat-----tgtacttttatttcagAGAAAATCAGAAGAAGTTCTGTTCTACTTGAACGGGAGGTGTATTTACCTAGTAG
















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|218500073|gb|FG957690.1|FG957690
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|29687750|gb|CB684025.1|CB684025
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|29661027|gb|CB657302.1|CB657302
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|88333298|gb|CI642335.1|CI642335
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|58599198|gb|CK009726.1|CK009726
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|29660283|gb|CB656558.1|CB656558
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|58674778|gb|CK063465.1|CK063465
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|58587730|gb|CF986038.1|CF986038
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|58603248|gb|CK013776.1|CK013776
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|55409593|gb|CV721969.1|CV721969
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|29660344|gb|CB656619.1|CB656619
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|5004551|gb|AU069726.1|AU069726
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|58612291|gb|CK040003.1|CK040003
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
EST: gi|29636670|gb|CB641679.1|CB641679
EST:     GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAG                         AGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA
genomic: GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTA

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: 47 (upstream exon), 55 (downstream exon)
Score: 41

GTCATGAAACATTGCATAACTCGGTTGATGAAGCCCTCTTGCTAAAGgtactgcata ... ttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTAGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgcttgttttcttccatcactctatgttctaaccatctgttttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTAGTTG
                              ttctaac  putative branch site (score: 41)
                                       tctgttttattttc  putative PPT
                                      atctgttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcataatcaaatcaaaggcgacactggagtttgcttgttttcttccatcactctatgttctaaccatctgttttattttcagAGAAAATCAGAAGAAGTTCTCTTCTATTTGAATGGACGGTGTATTTACCTAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT