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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttctattgtgtttgaattttgaaccaacttatgctatttgggaagcactgatttgttgttatcttgcttcgttgtgactgtggtttgtgaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTA

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 1
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|88396973|gb|CI578122.1|CI578122
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29646523|gb|CB651530.1|CB651530
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58608259|gb|CK036292.1|CK036292
EST:     CTGCGGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58669315|gb|CK058001.1|CK058001
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88717707|gb|CI741217.1|CI741217
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29673248|gb|CB669523.1|CB669523
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58659150|gb|CK047830.1|CK047830
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29641723|gb|CB646730.1|CB646730
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29624841|gb|CB629852.1|CB629852
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88360099|gb|CI610213.1|CI610213
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|11610396|gb|AU166072.1|AU166072
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88315187|gb|CI611851.1|CI611851
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88728131|gb|CI751641.1|CI751641
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29673598|gb|CB669873.1|CB669873
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58685697|gb|CK074384.1|CK074384
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58670226|gb|CK058912.1|CK058912
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTT-C--CG                         -T-C-GCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58672680|gb|CK061366.1|CK061366
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGACAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|29616238|gb|CB621250.1|CB621250
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88356602|gb|CI626217.1|CI626217
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88696183|gb|CI739758.1|CI739758
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58691339|gb|CK080026.1|CK080026
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58666569|gb|CK055255.1|CK055255
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58690262|gb|CK078949.1|CK078949
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88405374|gb|CI586195.1|CI586195
EST:     TGCTGCGGGGGAGATCTGTCCGGGGTGTGCGGCTGATTCGC-TTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: TGCTGCGGGGGAGATCTGTCC-GGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58687148|gb|CK075835.1|CK075835
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58680355|gb|CK069042.1|CK069042
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58601351|gb|CK011879.1|CK011879
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|88445013|gb|CI589491.1|CI589491
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
EST: gi|58605686|gb|CK033719.1|CK033719
EST:     CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCG                         CTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG
genomic: CTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGG

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: 32 (upstream exon), 63 (downstream exon)
Score: 8

CGGCTTCGTCCCCGCCGCCGTACTGCGCCGCCGCCGGTGCCGACCTGCTGCTGCTGCGGGGGAGATCTGTCCGGGTGTGCGGCTGATTCGCTTTCCGTCGgtacgatttc ... gaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcactgatttgttgttatcttgcttcgttgtgactgtggtttgtgaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTA
  cactgat  putative branch site (score: 8)
       atttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctattgtgtttgaattttgaaccaacttatgctatttgggaagcactgatttgttgttatcttgcttcgttgtgactgtggtttgtgaatcgacagCTGCAGCTCTACAGGTTTCTTCGGCAGCAACTGTAGTAGAAAAGAAAGAGGGGAAGATTCGCAGTTCATATGGCAAAACCTGCTAATAGCATTGGCCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - tgtttga
- - - - - - - - - - - gaaccaa
- - - - - - - - - - - - - - -cttatgc
- - - - - - - - - - - - - - - - - - - - - - - gcactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactg