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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactacctcatatatgctttacttgcagaatcctaaaattacttctgatccaaaaagattatactagtaggagtatcgcacagtcctaactgtttctgaattctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g60830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G027478_T02 (Zea mays), 3'ss of exon 2
gtactacctcatatatgctttacttgcagaatcctaaaattacttctgatccaaaaagattatactagtaggagtatcgcacagtcctaactgtttctgaattctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG
            | ||   ||| | ||| |   |     ||| | || | | | | ||| |||     ||          ||   |  |||    | ||  |||   || |||| |||||| ||||||| ||||| |||||||| || |||||||||||  | |||||||||||||| || ||||| || |||||||| ||||||||||||||
--------ctgaaaatatatta-tcgcacacatccttttttattcctaa-caagagagaatatcaagttatcgacgattgacgacc--aaccaaat-tggtttcgaatttcagTCGACGGGCAATACGTGGAGGAGGGTTGGGTCGACAAGACCTGCAAGATCTGCAAGAAGGACACAAGGGGGGAGCCGAGGCAGGTTGACAAGCTAGGAAG

upper sequence: LOC_Os01g60830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0067g02560.t01 (Vitis vinifera), 3'ss of exon 2
gtactacctcatatatgctttacttgcagaatcctaaaattacttctgatccaaaaagattatactagtaggagtatcgcacagtcctaactgtttctgaattctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG
   |||   || ||  || |   || |  |||| |   ||   |  |  |||  |||| ||     |  |   || | |  || | |   ||   |   |||        |||| || ||  ||||||| ||||| |||||||| ||||| ||||||||||| |||||| ||||||| |||||||||||||||||||| |||||| | |||||
--gctatg-caaatgagcctgcattacc-aatctttccatgtttgattttcctcaaagtttcctgcaa-accggttttgatcaattcagtcttgcttgaaat--------cagTGGATGGACAATACGTCGAGGAGGGTTGGGTCGATAAAACCTGCAAAGTATGCAAGGAGGACACCAGAGGGGAACCCAGGCAGGTGGACAAGTTTGGAAG

upper sequence: LOC_Os01g60830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S20_237V6.1 (Physcomitrella patens), 3'ss of exon 2
gtactacctcatatatgctttacttgcagaatcctaaaattacttctgatccaaaaagattatactagtaggagtatcgcacagtcctaactgtttctgaatt--ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG
            |   |    | | || | ||  || ||| |  ||  |||| |  |   |  || | |    |  |||     | |  ||  || |   |||  ||||| |||||||| ||||  ||||| || ||||||||||| || || |||||||||   |||||||||||||| | ||| |  ||| |       |||      ||| |
-----------caacagtcacagtagc-gtatgttacaataatatcatatccgatta--ctcaacgattgaacgactcgtttcatacctacaattgcccgattgactgct-gcagTTGATGGGGCGTACGTGGACGAAGGTTGGGTCGACAAAACCTGCAAATACTGCAAGAAGGACACGAAAGGTGCTCCCCGAACTAAGGACTCAAGTGGACG

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|88369115|gb|CI678640.1|CI678640
EST:     GAGGAAGATCAGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGG
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGG
EST: gi|88662178|gb|CI465970.1|CI465970
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88459334|gb|CI517012.1|CI517012
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88438317|gb|CI541061.1|CI541061
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|55413504|gb|CV725880.1|CV725880
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|33666797|gb|CF297764.1|CF297764
EST:     AGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATTATGTGGATG                         TTGACAGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: AGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCAT-ATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|112786877|gb|EE591615.1|EE591615
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|55437018|gb|CV731706.1|CV731706
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88663015|gb|CI477119.1|CI477119
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|33664957|gb|CF295924.1|CF295924
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88661567|gb|CI456679.1|CI456679
EST:     GAGGAAGATCAGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|38480356|gb|CF964445.1|CF964445
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88663304|gb|CI478414.1|CI478414
EST:     GAGGAAGATCAGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACNTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88662596|gb|CI470600.1|CI470600
EST:     GCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|38478506|gb|CF962639.1|CF962639
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88663584|gb|CI483448.1|CI483448
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|55413503|gb|CV725879.1|CV725879
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88663812|gb|CI486873.1|CI486873
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATNTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|55437876|gb|CV732230.1|CV732230
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88662280|gb|CI464463.1|CI464463
EST:     GAGGAAGATCAGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|33677254|gb|CF305493.1|CF305493
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGGTTGGGTGGATAAGACCTGCAAAGTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGG-TTGGGTGGATAAGACCTGCAAAGTT
EST: gi|33663240|gb|CF294207.1|CF294207
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88453609|gb|CI681844.1|CI681844
EST:     GAGGAACATCGGTGGCACCTACAAGGATTTCTTCCAGTCATATGTGGATG                         TTGACGGGGAATAAC-TACAGGAAGGTTGGGTGGA
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATA-CGTAGAGGAAGGTTGGGTGGA
EST: gi|313079211|gb|HO663792.1|HO663792
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88566846|gb|CI497563.1|CI497563
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|55437016|gb|CV731705.1|CV731705
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|33676980|gb|CF305219.1|CF305219
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|4716749|gb|AU057865.1|AU057865
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|55437874|gb|CV732229.1|CV732229
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88661696|gb|CI457387.1|CI457387
EST:     GAGGAAGATCAGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88664313|gb|CI687101.1|CI687101
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAG
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAG
EST: gi|33676945|gb|CF305184.1|CF305184
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|33666798|gb|CF297765.1|CF297765
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACAGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88664469|gb|CI697724.1|CI697724
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTA
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTA
EST: gi|88662688|gb|CI472250.1|CI472250
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88304002|gb|CI513076.1|CI513076
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|88663387|gb|CI481484.1|CI481484
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAATTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
EST: gi|55434716|gb|CV730482.1|CV730482
EST:     GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATG                         TTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT
genomic: GAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTT

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: 70 (upstream exon), 69 (downstream exon)
Score: 141

TATGGAGCACTTCGGAGGAAGATCGGTGGCACCTACAAGGATTTCTTCAAGTCATATGTGGATGgtactacctc ... ctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatactagtaggagtatcgcacagtcctaactgtttctgaattctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG
                          tcctaac  putative branch site (score: 141)
                                           ttctgctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactacctcatatatgctttacttgcagaatcctaaaattacttctgatccaaaaagattatactagtaggagtatcgcacagtcctaactgtttctgaattctgcttgcagTTGACGGGGAATACGTAGAGGAAGGTTGGGTGGATAAGACCTGCAAAGTTTGCAAGAAGGACACTAGAGGGGAACCCAGGCAGGTCGACAAGCTAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT