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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcttccttgcttaaatacttattccaagagacagcaaagccaaaatagaaattgactgttactaattgattcgctattcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCTGGAGCTGTCCGTGTTCACGAGGATATGCTTCTAGCTGCCT

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 17
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|86519891|gb|CI160097.1|CI160097
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGACTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29668943|gb|CB665218.1|CB665218
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|58689010|gb|CK077697.1|CK077697
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|218502213|gb|FG961004.1|FG961004
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29640538|gb|CB645547.1|CB645547
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|58604549|gb|CK015077.1|CK015077
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|86594283|gb|CI251155.1|CI251155
EST:     AAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCGCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: AAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29642463|gb|CB647470.1|CB647470
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|218479902|gb|FG948663.1|FG948663
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAAATGCCTACATTTTCCCCTGGATTCGGCCTCGGTGTTGTAATCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAA-TGCCTACATTTTCCC-TGGATTCGGCCTCGGTGTCGTAATCT
EST: gi|87040607|gb|CI195229.1|CI195229
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|218493259|gb|FG949070.1|FG949070
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|88198812|gb|CI197209.1|CI197209
EST:     GTCCGTTGGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|58671293|gb|CK059979.1|CK059979
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29630820|gb|CB635829.1|CB635829
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|88961240|gb|CI096644.1|CI096644
EST:     GTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29663066|gb|CB659341.1|CB659341
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29625639|gb|CB630650.1|CB630650
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|38474181|gb|CF958313.1|CF958313
EST:     GTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|58673473|gb|CK062159.1|CK062159
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|89184779|gb|CI048335.1|CI048335
EST:     CGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: CGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|89197307|gb|CI052037.1|CI052037
EST:     GAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCGCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|87041398|gb|CI196020.1|CI196020
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTT-CCTGGANTTCGGCCTCGGTGTCGTAATCTC
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGA-TTCGGCCTCGGTGTCGTAATCTC
EST: gi|58585822|gb|CF984130.1|CF984130
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29645566|gb|CB650573.1|CB650573
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29626361|gb|CB631372.1|CB631372
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|15858197|gb|BI811009.1|BI811009
EST:     TGACCCTGTGGAGTACACATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATGTTTCCCCTGGATTCGGCCTCGGTGTTGTAATCT
genomic: TGACCCTGTGGAGTACA-ATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACAT-TTT-CCCTGGATTCGGCCTCGGTGTCGTAATCT
EST: gi|87041092|gb|CI195714.1|CI195714
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|89195350|gb|CI051463.1|CI051463
EST:     GTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCNTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29681753|gb|CB678028.1|CB678028
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|29626362|gb|CB631373.1|CB631373
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|86518820|gb|CI159026.1|CI159026
EST:     CTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAAGGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: CTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|218502862|gb|FG946696.1|FG946696
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|88248955|gb|CI248804.1|CI248804
EST:     ATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: ATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|88197857|gb|CI197707.1|CI197707
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|58679004|gb|CK067691.1|CK067691
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|218497744|gb|FG966597.1|FG966597
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTTGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|88198739|gb|CI198589.1|CI198589
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCGTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|8956808|gb|BE230611.1|BE230611
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
EST: gi|86519039|gb|CI159245.1|CI159245
EST:     GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG                         TCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT
genomic: GTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCT

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), 75 (downstream exon)
Score: 136

GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAGgtactgcttc ... ttcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCTGGAGCTGTCCGTGTTCACGAGGATATGCTTCTAGCTGCCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcaaagccaaaatagaaattgactgttactaattgattcgctattcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCTGGAGCTGTCCGTGTTCACGAGGATATGCTTCTAGCTGCCT
          aaaatagaaattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcttccttgcttaaatacttattccaagagacagcaaagccaaaatagaaattgactgttactaattgattcgctattcacaacagTCGAACAATGCCTACATTTTCCCTGGATTCGGCCTCGGTGTCGTAATCTCTGGAGCTGTCCGTGTTCACGAGGATATGCTTCTAGCTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC