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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgacttgctttatatgacaatatttttattatggcaattgcaagtatctttaggttcaagttccattgaaagttttattggtatctgtactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAATCTGGCTTCTGTCAGTGAAGATAGTGTCAGAATATGGTCGTTTGCTCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g42260.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G425377_T01 (Zea mays), 3'ss of exon 8
--------atatgacttgctttatatgacaatatttttattatggcaattgcaagtatctttaggttcaagttccattg-aaagttttattggtatctgtactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAATCTGGCTTCTGTCAGTGAAGATAGTGTCAGAATATGGTCGTTTGCTCCTG
        |    | ||  |||   | | |||    |   | | ||| |||  |  |    |  ||     |   | || |||| | | ||     ||  | | ||||||||||||  ||||||||||| || ||||||||||||||| | || ||  |||| |||||||||||||||||    |||||||||||||| ||   | |||
tttacgatactgaatttcatttgatttaaaatgagatctgttttgcatttggcaacaaaactgagt----atctaactgtaaaggtctgtt-----ctcaaatgtgtagGGGCACAATAAGAATATTCAATCGCTTTGTTGGGATTCTGCTGGCGAATATCTCGCTTCTGTCAGTGAAGACTCGGTCAGAATATGGTCATTCAGTTCTG

upper sequence: LOC_Os01g42260.3 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 16
-atatgacttgctttatatgacaatatttttattatggcaa---ttgcaagtatctttaggttcaagttcc--attg-aaagttttattggtatctgtactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAATCTGGCTTCTGTCAGTGAAGATAGTGTCAGAATATGGTCGTTTGCTCCTG
  |||||  ||||  || | |    ||||  | |  |  ||   |||||  |  |   |       ||  |  |  | |||| ||| ||     ||  | | ||||||||||||  ||||||||||| || ||||||||||| ||| | |||||  ||||||||||||||||||||||    |||||||||||||| ||   | |||
tttatga--tgctgaatttcatctgatttaaaatgagataagttttgcatttggcaacaaaactgggtatctaaccgtaaaggtttgtt-----cttaaatgtgtagGGGCACAATAAGAATATTCAATCGCTTTGTTGGGACTCTGCTGGTGAATATCTGGCTTCTGTCAGTGAAGACTCAGTCAGAATATGGTCATTCAGTTCTG
















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|88221810|gb|CI221766.1|CI221766
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|16576984|gb|BI804280.1|BI804280
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACAC-AAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGAC-AT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|29681692|gb|CB677967.1|CB677967
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|4714252|gb|AU058219.1|AU058219
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAA
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCA-Ggtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAA
EST: gi|86430973|gb|CI083396.1|CI083396
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|86431296|gb|CI083719.1|CI083719
EST:     TCGACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|33690022|gb|CF318261.1|CF318261
EST:     ACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: ACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|58682276|gb|CK070963.1|CK070963
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|86260005|gb|CI065878.1|CI065878
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGGCAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|33690021|gb|CF318260.1|CF318260
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|88842163|gb|CI081419.1|CI081419
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|8404601|gb|AU091955.1|AU091955
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTNTAGAAACCCTCTGCNG                         GGGCACACAAAGNATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|16575961|gb|BI803257.1|BI803257
EST:     TCTACATACTTGATGGAGAGACAC-ACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACAC-AAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGAC-AT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|29673281|gb|CB669556.1|CB669556
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|218488081|gb|FG946110.1|FG946110
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|29638960|gb|CB643969.1|CB643969
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
EST: gi|38478243|gb|CF962376.1|CF962376
EST:     TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAG                         GGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT
genomic: TCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAAT

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: 62 (upstream exon), 74 (downstream exon)
Score: 47

ATTTCAACCTCAAAAGGGAAAATATCTTGCAGCTGCCTCAGAGAAGGCCATCTACATACTTGATGGAGAGACACAACTTGCTTGTAGAAACCCTCTGCAGgtctgttagc ... tactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAATCTGGCTTCTGTCAGTGAAGATAGTGTCAGAATATGGTCGTTTGCTCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatctttaggttcaagttccattgaaagttttattggtatctgtactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAATCTGGCTTCTGTCAGTGAAGATAGTGTCAGAATATGGTCGTTTGCTCCTG
                      attgaaagttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgacttgctttatatgacaatatttttattatggcaattgcaagtatctttaggttcaagttccattgaaagttttattggtatctgtactctgtagGGGCACACAAAGAATATTCACTCACTTTGTTGGGATTCTACCGGTGACAATCTGGCTTCTGTCAGTGAAGATAGTGTCAGAATATGGTCGTTTGCTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA