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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctcctgctgcttcacagcatgatttccatatgttctaaagattactgagtcatattcaacgctagcgctctaatggcgaaattgcaatgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCCGAGGTGGGAGGTCCCCTACAACCTTCTCCAGAGGGAGCCAGCCCCGCCC

Basic information

species Oryza sativa
transcript LOC_Os01g03950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03950.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G009282_T01 (Zea mays), 3'ss of exon 1
gtgctcctgctgcttcacagcatgatttccatatgt-tctaaagattactgagtcatattcaacgctagc---gctctaatggcgaaattgcaatgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCCGAGGTGGGAGGTCCCCTACAACCTTCTCCAGAGGGAGCCAGCCCCGCCC
    ||      ||||  | || ||  ||    | |  || ||  || |   | | ||   ||   || |   | ||   |    |   ||  | |||  ||||||||||||||| ||| ||| | || || ||||| || || ||||| |||| |||||||||||||||||||||||| ||||  |||||||||||||| |||
----tctaaagacttccaatcacgagctcagagtatgcctgaactttgcgatggcttaaaaaaaattatccgaggtcatcttctaatggtgagacgctatgcagGCACGAGACCAGGGAGAGGGTGCGCGTGCAGATTACAGATGCAGATAAGCAGAGGTGGGAGGTCCCCTACAACCTGCTCCCAAGGGAGCCAGCCCCACCC
















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|58653313|gb|CK041993.1|CK041993
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88421835|gb|CI611714.1|CI611714
EST:     CGCACCTCCACCTACGGCCCGGACATCC-TCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88335222|gb|CI658229.1|CI658229
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGA
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGA
EST: gi|88355066|gb|CI615947.1|CI615947
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCA
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCA
EST: gi|88390377|gb|CI607413.1|CI607413
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGAAAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88569643|gb|CI660818.1|CI660818
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88364076|gb|CI610420.1|CI610420
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88399485|gb|CI606106.1|CI606106
EST:     CGCACCTCCACCTACGGCCCGGAAATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGAAAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88346538|gb|CI622995.1|CI622995
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88296423|gb|CI669199.1|CI669199
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|58669270|gb|CK057956.1|CK057956
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88350017|gb|CI621948.1|CI621948
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGAAAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88402770|gb|CI613218.1|CI613218
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88395271|gb|CI611188.1|CI611188
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88346665|gb|CI624318.1|CI624318
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88396803|gb|CI620136.1|CI620136
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88364065|gb|CI610409.1|CI610409
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCAAGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|88316434|gb|CI621673.1|CI621673
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|58663552|gb|CK052238.1|CK052238
EST:     GCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCGTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: GCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGC-TCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
EST: gi|58657510|gb|CK046190.1|CK046190
EST:     CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAA                         GCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC
genomic: CGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCC

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: 74 (upstream exon), 73 (downstream exon)
Score: 7

TCGAGCACCCCGAGGGAGGAGCTCTCGTTGGATACCTGCAGGTGAAGCAGCGCACCTCCACCTACGGCCCGGACATCCCTCTCCTCAGGCTCTATGTCAAgtaagaacag ... tgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCCGAGGTGGGAGGTCCCCTACAACCTTCTCCAGAGGGAGCCAGCCCCGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgagtcatattcaacgctagcgctctaatggcgaaattgcaatgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCCGAGGTGGGAGGTCCCCTACAACCTTCTCCAGAGGGAGCCAGCCCCGCCC
                         ctctaat  putative branch site (score: 7)
         atattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctcctgctgcttcacagcatgatttccatatgttctaaagattactgagtcatattcaacgctagcgctctaatggcgaaattgcaatgctgcgcagGCACGAGACCAAGGACAGGATACGAGTCCAGATCACGGACGCAGACAAGCCGAGGTGGGAGGTCCCCTACAACCTTCTCCAGAGGGAGCCAGCCCCGCCC

gtgctcc
- - - -tgctgct
- - - - - - - - - agcatga
- - - - - - - - - - - - - - -catatgt
- - - - - - - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattgca