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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgctaatgcacatatttgagtattcatagatttaccccggaaaagttgcattgatgattcttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATT

Basic information

species Oryza sativa
transcript LOC_Os07g49270.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49270.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G134396_T03 (Zea mays), 3'ss of exon 14
gtatatgctaatgcacatatttgagtattcatagatttaccccggaaaagttgcattgatgattcttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATT
||   |||  |  || | | |  |  ||    || |  | |  | |   | || | | ||  || || |||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||| |||||||| ||||| ||  ||||||| |||||||| || ||||| |||||||
gttagtgccta-acataaactataa-atctccaggtcgaacttgaacttggtgaacttattgttgttatcttcagGCTGGTGATATCGATCACCTTGCTGCAGCATTTCTTACTTCACATAACATTGCTCATGGGGTGAACCTAAAGAAATCCCCTGTACTTCAGTACCTGTATT
















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|58694980|gb|CK083667.1|CK083667
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|86871926|gb|CI332098.1|CI332098
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|86599171|gb|CI355788.1|CI355788
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|29671780|gb|CB668055.1|CB668055
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88276104|gb|CI396708.1|CI396708
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|33675288|gb|CF303527.1|CF303527
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|29663749|gb|CB660024.1|CB660024
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88901869|gb|CI374477.1|CI374477
EST:     GTGAGTCCAAGGGTATGACAACAATCAGACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|218478545|gb|FG960299.1|FG960299
EST:     CACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: CACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|58593125|gb|CF991433.1|CF991433
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATGGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88265236|gb|CI369010.1|CI369010
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88906500|gb|CI375572.1|CI375572
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|86602782|gb|CI357146.1|CI357146
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88970069|gb|CI383571.1|CI383571
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88263167|gb|CI366941.1|CI366941
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88835899|gb|CI371004.1|CI371004
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|163926592|gb|EG713608.1|EG713608
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|88839179|gb|CI378103.1|CI378103
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|89196317|gb|CI397319.1|CI397319
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATACT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATA-T
EST: gi|86889206|gb|CI315817.1|CI315817
EST:     TGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACCTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: TGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACAC-TGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
EST: gi|86883261|gb|CI328682.1|CI328682
EST:     GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAG                         GCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT
genomic: GTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATT

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: 54 (upstream exon), 51 (downstream exon)
Score: 24

CTTCGTGAGTCCAAGGGTATGACAACAATCAAACTTCGTCCACACTGTGGGGAGgtatatgcta ... ttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgagtattcatagatttaccccggaaaagttgcattgatgattcttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATT
                                 cattgat  putative branch site (score: 24)
                                          ttcttgtcttc  putative PPT
     tattcatagattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgctaatgcacatatttgagtattcatagatttaccccggaaaagttgcattgatgattcttgtcttcagGCTGGAGATATTGATCATCTTGCTGCAGCATTTCTTACTTCTCATAATATTGCTCACGGGGTTAATTTAAAGAAGTCCCCTGTCCTCCAGTATCTGTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT