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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAGACTTCTACTGTTCGGTTGACAAGGTACAAGGTGCTGATGGAAAAGATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttttcttgcttccctattctcgatataatcatcttacttttttgaattgatgcataattgaatatgttgaatcatctgccgtctgtatggaag...

Basic information

species Oryza sativa
transcript LOC_Os10g33270.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33270.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 3
TATAGACTTCTACTGTTCGGTTGACAAGGTACAAGGTGCTGATGGAAAAGATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttttcttgcttccctattctcgatataatcatcttacttttttgaat-tgatgcataattgaatatgttgaatcatctgccgtctgtatggaag-
 ||||||||||| ||||| |||||||||||  |||| || || ||||||||||| ||||||||||||||||||||||| ||||| ||||||| ||| |||||  |||| ||||| ||      ||   | |   |   | |||||| || |    || |||  || ||   |  |  |      |||   |  |||   |  
CATAGACTTCTATTGTTCAGTTGACAAGGTTGAAGGGGCCGACGGAAAAGATCGTGTGGTGGTCACATTTGATGGGAAGTATCTACCTTACACTGAACAGgtccgtgtcttcttcctgttt--tttcagctgccactctgttacttgttagctcatggtgctgaactgctgaactgcatctgcttgctagccatataatacc

upper sequence: LOC_Os10g33270.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv05s0049g01520.t01 (Vitis vinifera), 5'ss of exon 3
TATAGACTTCTACTGTTCGGTTGACAAGGTACAAGGTGCTGATGGAAAAGATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagt---gttttcttgc--ttccctattctcgatataatcatcttacttttttgaattgatgcataattgaatatgttgaatcatctgccgtctgtatggaag
 |||||||||||||| || |||||||| ||  ||||||  |||||||| ||||| |||||  | || ||||||||||| ||| | ||| | |  |||||||| |||    ||||| | |  ||    ||| | | |   ||   || | |  |   || | |   ||||   || |||   | |  |    | |  |||  ||  
CATAGACTTCTACTGCTCAGTTGACAAAGTTAAAGGTGTGGATGGAAAGGATCGTGTGGTCTTGACGTTTGATGGGAAGTATTTGCCTCATACAGAGCAGgtcagttgcattttcgtacagttagaaattgttgttggcatacactgaatcat--aaaataaaaaataag-aaaaatgaaaattagttgaacattagtagtga--
















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|88292276|gb|CI500224.1|CI500224
EST:     ATCGCNTGGTGTTCACATTTGATGGG-AATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGGTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|86484118|gb|CI126751.1|CI126751
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACCGTGAGCAG                         AGATCTGATCATATGAGGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|87010351|gb|CI281241.1|CI281241
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88527082|gb|CI455199.1|CI455199
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88998230|gb|CI038115.1|CI038115
EST:     CATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: CATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88537579|gb|CI466540.1|CI466540
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88474979|gb|CI412250.1|CI412250
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         ANATCTGATCATATGATGTTTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|86535937|gb|CI176143.1|CI176143
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGTTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88513993|gb|CI441499.1|CI441499
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|11025781|gb|AU162382.1|AU162382
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88514379|gb|CI441885.1|CI441885
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|86254024|gb|CI058751.1|CI058751
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|25798783|gb|CA754744.1|CA754744
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|58693386|gb|CK082073.1|CK082073
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88439725|gb|CI541282.1|CI541282
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTTTAGNCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88463661|gb|CI696136.1|CI696136
EST:     TCGCGTGGTGGTCACCATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCCGATCCCATGATGTCTACGCTGACCCGC
genomic: TCGCGTGGTGGTCAC-ATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGC
EST: gi|427738|gb|D23873.1|D23873
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88578606|gb|CI687547.1|CI687547
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTCCCTTACAGTGAGCAG                         AGATCTGATCATATGA
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGA
EST: gi|88514316|gb|CI441822.1|CI441822
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88979062|gb|CI025570.1|CI025570
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|86418185|gb|CI032394.1|CI032394
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88998125|gb|CI038010.1|CI038010
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|88545694|gb|CI475273.1|CI475273
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|86855243|gb|CI265169.1|CI265169
EST:     ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
EST: gi|86533060|gb|CI173266.1|CI173266
EST:     GTCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAG                         AGATCCGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC
genomic: ATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGC

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: 75 (upstream exon), 62 (downstream exon)
Score: 150

TATAGACTTCTACTGTTCGGTTGACAAGGTACAAGGTGCTGATGGAAAAGATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttt ... atatttgcagAGATCTGATCATATGATGTCTAGGCTGACCCGCAAGACATCTTGAGATGGCTGGTGTTGTGGGAAAAATGATGTATCATCTGCTTCTGCTTGTGGATTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAGACTTCTACTGTTCGGTTGACAAGGTACAAGGTGCTGATGGAAAAGATCGCGTGGTGGTCACATTTGATGGGAAATATCTTCCTTACAGTGAGCAGgttagtgttttcttgcttccctattctcgatataatcatcttacttttttgaattgatgcataattgaatatgttgaatcatctgccgtctgtatggaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG