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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatcctactccctctgtccctaaatataagggattttggttggatggtctagattcgtagtactaagatacgtcacatccaaccaaaatccttt...

Basic information

species Oryza sativa
transcript LOC_Os01g37770.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37770.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G015364_T02 (Zea mays), 5'ss of exon 9
GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatcc------tactccctctgt----ccctaaatataagggattttggtt---ggatggtctagattcgtagtactaagatacgtcacatccaaccaaaatccttt------------------------------------------------------
 ||||||||||| ||||||||||||||  | ||||||||||||||| | ||| | |||||||||||||||||||||||| || ||||   ||  ||      |||| ||| | |     || | |||  |    ||| |  |   || | || |       | | | | || ||  ||||||| | | |      | |                                                      
ACTTATGCCAGATTCAGCTCTTACAGCCACAAAGGAAAAGAAACTCACGGGACGGCAGTATTTTGAAAGTGGAAGGCATGCAGTGgtttgtatcccagataatactacctttttgttatcccagataataaaactttcgtctcaaggcttgtttgatgcactcgcattcagctat-tcacatcaatctatgtgtgtgttggagttacttacgtgtcttttaagttctactttacatgaagccatcttttcag

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G094595_T04 (Zea mays), 5'ss of exon 8
GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatcctactccctctgtccctaaatataagggattttggttggatggtctagattcgtagtactaagat-acgtcacatcca-accaaaatccttt-------------------------------------------
 ||||||||||| |||||||||||| |  | ||||||||||||||| ||||| | |||||||||||||||||||||||| || |||| | | |||| |     |    || |   | |||||    ||| |||||||  || |  |     || | | || |  |||  ||        |      |                                           
ACTTATGCCAGATTCAGCTCTTACATCCTCAAAGGAAAAGAAACTCACAGGACGGCAGTATTTTGAAAGTGGAAGGCATGCAGTGgttcgttatcccagataataaaacctttcct-taagg---cttgtttggatgcactcgtatttagttatttacatcaattcatgtctgtgttggagctacgtatgtgtcttttacgttttactttacatgaaaccatcttttcag

upper sequence: LOC_Os01g37770.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g02540.t01 (Vitis vinifera), 5'ss of exon 9
GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatcctactcc-----ctctgtccctaaatataagggattttggttggatggtct--agattcgtagtactaagatacgtcacatccaaccaaaatccttt
||| ||||| ||||| || ||||||||||| ||||||||||| |||||||| |||||||  ||||||||||||||   |  |  ||||||| ||||| | ||      ||    |  | ||   ||     | |  |   || |||  | ||| | |  ||| | |||| |    |  ||  |||||     
GCTAATGCCCGAGTCTGCACTTACAGCTCCCAAGGAAAAGAAGCTCTCAGGCAGACAGTGGTTTGAAAGTGGAAGAGCTGTAGCGgtactttatcctcccccaaactttcctctctcagattgcagatgcatggaatttgtgttcttcacatttg-aaaactcatatac-tattgttgaaataaaat-----

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|55410164|gb|CV722540.1|CV722540
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|88353314|gb|CI654580.1|CI654580
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|29670377|gb|CB666652.1|CB666652
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCCCTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|89186245|gb|CI262077.1|CI262077
EST:     AGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|88491923|gb|CI429195.1|CI429195
EST:     ACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: ACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|29670376|gb|CB666651.1|CB666651
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|88457374|gb|CI534372.1|CI534372
EST:     CAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: CAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|88958850|gb|CI381653.1|CI381653
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAAACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|86880817|gb|CI339152.1|CI339152
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|33665592|gb|CF296559.1|CF296559
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|86602635|gb|CI356999.1|CI356999
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|86885488|gb|CI318639.1|CI318639
EST:     AAGAAACTCTCAGGAAGACAGTAGTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|86889359|gb|CI317159.1|CI317159
EST:     TGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: TGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|218496890|gb|FG962706.1|FG962706
EST:     AAAAGAAACTCTCAGCAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|88250975|gb|CI349205.1|CI349205
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|88255347|gb|CI354171.1|CI354171
EST:     TGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: TGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
EST: gi|87010761|gb|CI312453.1|CI312453
EST:     AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATG                         AAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC
genomic: AAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATC

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: 50 (upstream exon), 66 (downstream exon)
Score: 14

GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatc ... ttctttccagAAAGGAGCAAGTACCACTGCTGACGAAGAGGAGGAAGAAGAGGAAGACATCGACTTTGATGAAGACTTCGATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTATGCCAGAGTCAGCTCTTACAGCTCCGAAGGAAAAGAAACTCTCAGGAAGACAGTATTTTGAAAGTGGAAGGCATACAATGgtacttaatcctactccctctgtccctaaatataagggattttggttggatggtctagattcgtagtactaagatacgtcacatccaaccaaaatccttt

- - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctc