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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggatgtctagcttttgtattgtgatttcttgttacaatattctagctagagcaaccaaattctgaactcaatgggactacttttttttgtaaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCTTCGAGGATGCATTGGAACCTTGGAGGCTCGTCAGATTGTCACTGGCTTC

Basic information

species Oryza sativa
transcript LOC_Os10g42250.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42250.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G131667_T01 (Zea mays), 3'ss of exon 1
--aggatgtctagcttttgt--attgtgatttcttgttacaatattctagctagagcaaccaaattctgaactcaatgggactacttttttttgtaaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCTTCGAGGATGCATTGGAACCTTGGAGGCTCGTCAGATTGTCACTGGCTTC
       || |||      |  |||   ||  ||||| |    ||  | | |  ||||  ||  || | |||||| |||| | | |||||| |   ||||| |||||||||||||| ||||||||||||||| |||||||||||||||||||||| || |||||||| |||||  ||||| | |||||||||||||  ||||| 
ttcaaccgtgtagtccacattaatttgtatggcttgt-aaggcatcattgttctagcatacatgtttttaactcattgggtcaatttttttgt---aactttagCCCATTGTTTGTGACCTGGAAGAAGGCTGCCAATGGTTCAGAACCACGCCTCCGGGGATGCATAGGAACTCTGGAGTCCCGTCAGATTGTCAGCGGCTTT
















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|2428016|gb|C72479.1|C72479
EST:     CACTACAGCGGCGACCAG-CGACGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88736026|gb|CI759534.1|CI759534
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|58591535|gb|CF989843.1|CF989843
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCC
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACC-TGGAAGAAGGCTACCAATGGTTCAGAACCACGCC
EST: gi|55433330|gb|CV729741.1|CV729741
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|33680238|gb|CF308477.1|CF308477
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|44668540|gb|CR281974.1|CR281974
EST:     CACTACAGCGGCGACGAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|33814577|gb|CF333153.1|CF333153
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|55435942|gb|CV731108.1|CV731108
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|66931214|gb|CX118062.1|CX118062
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88370111|gb|CI585116.1|CI585116
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|58602145|gb|CK012673.1|CK012673
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGGTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|55415462|gb|CV727838.1|CV727838
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88417365|gb|CI579026.1|CI579026
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88693360|gb|CI736935.1|CI736935
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88744786|gb|CI768146.1|CI768146
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88405487|gb|CI588693.1|CI588693
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|218485154|gb|FG948395.1|FG948395
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|33812402|gb|CF332089.1|CF332089
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88417381|gb|CI579042.1|CI579042
EST:     CACTACAGCGGGGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|58657144|gb|CK045824.1|CK045824
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGG-GGGCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
EST: gi|88572682|gb|CI664253.1|CI664253
EST:     CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCA                         CCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT
genomic: CACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCT

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: 68 (upstream exon), 66 (downstream exon)
Score: 5

TGGTGGCCACGGAGGAAATGGCGGTCTACTGCTTCGACGCCCTCGTCTCCCACTACAGCGGCGACCAGCCGCCGCCGCCCGCCTTCGAGGAGGGCATCCAgtaagcaccc ... taaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCTTCGAGGATGCATTGGAACCTTGGAGGCTCGTCAGATTGTCACTGGCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagagcaaccaaattctgaactcaatgggactacttttttttgtaaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCTTCGAGGATGCATTGGAACCTTGGAGGCTCGTCAGATTGTCACTGGCTTC
                                ctacttttttttgt  CT-rich tract
                                 tacttttttttgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggatgtctagcttttgtattgtgatttcttgttacaatattctagctagagcaaccaaattctgaactcaatgggactacttttttttgtaaacttcagCCCATTGTTTGTCACCTGGAAGAAGGCTACCAATGGTTCAGAACCACGCCTTCGAGGATGCATTGGAACCTTGGAGGCTCGTCAGATTGTCACTGGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - -cttttgt
- - - - - - - - - -ttgtgat
- - - - - - - - - - - - - - - - - - - - - - - - - - caaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaatg