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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatccggactccggcatgatcaacctcgccacgcgcgcatttggcattcgcaatttcaggctctgaacatcggcttgacgactgaatggctgaatttttctcaacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACGCGACGGCTCGGGGATCACCGACGACGAGATCAAGCAGTACGTCGCAAAG

Basic information

species Oryza sativa
transcript LOC_Os08g34790.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34790.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G048522_T02 (Zea mays), 3'ss of exon 3
gtaagtatccggactccggcatgatcaacctcgccacgcgcgcatttggcattcgcaatttcaggctctgaacatcggcttgacgactgaatggctgaatttttctcaacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACGCGACGGCTCGGGGATCACCGACGACGAGATCAAGCAGTACGTCGCAAAG
    |||   || | ||  ||   ||  || |||  |   | |  | |  | | |||    || ||||| |||        ||||   |  |||    | |  | |   || |||||||||||||| || ||||||||||||||||| |||||||||||||| ||   || |||||| ||||||||||| |||||||||||||||||||| || || 
----gtaagtggccacccacaccgtcctccccgc-gcattctcgatcg--agttgca----caagctctaaac--------gacgttcgcttggt---actgctttgtccggtgcagAATGAAGGATGACTCCTGCGGCGAGATCCCGGTGGCGTTCGTCGTGGCGTCCGGCGGCTCCGGGATCACCGAGGACGAGATCAAGCAGTACGTGGCGAAA
















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|88330162|gb|CI658467.1|CI658467
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|88264952|gb|CI368726.1|CI368726
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|86498102|gb|CI140735.1|CI140735
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|87033821|gb|CI188445.1|CI188445
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|86525140|gb|CI165346.1|CI165346
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|86542814|gb|CI183020.1|CI183020
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|88479904|gb|CI417175.1|CI417175
EST:     GTCGCCNACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|86502493|gb|CI145126.1|CI145126
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|18387840|gb|BM421038.1|BM421038
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGATGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|88332567|gb|CI651727.1|CI651727
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|87006987|gb|CI275295.1|CI275295
EST:     GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: GAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
EST: gi|88202817|gb|CI200669.1|CI200669
EST:     CTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCC                         AATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG
genomic: CTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACG

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), 47 (downstream exon)
Score: 3

TCAAGGAGCTCATCAAGTACAAGGGCTTCCAGGTCGCCCCCGCCGAGCTCGAGGCCATGCTCATCGCCCACGCCGCCGTCGCCGACGCCGCCGTCGTCCCgtaagtatcc ... aacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACGCGACGGCTCGGGGATCACCGACGACGAGATCAAGCAGTACGTCGCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggctctgaacatcggcttgacgactgaatggctgaatttttctcaacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACGCGACGGCTCGGGGATCACCGACGACGAGATCAAGCAGTACGTCGCAAAG
               gcttgac  putative branch site (score: 3)
                                     tttttctca  putative PPT
                                 tgaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatccggactccggcatgatcaacctcgccacgcgcgcatttggcattcgcaatttcaggctctgaacatcggcttgacgactgaatggctgaatttttctcaacgatgcagAATGAAGGACGATTCCTGCGGCGAGATCCCAGTGGCGTTCGTCGTCGCACGCGACGGCTCGGGGATCACCGACGACGAGATCAAGCAGTACGTCGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG