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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagttacgattctctctcaaatgatgtgatcattgtagaaatatgcatctttgtccaacatatgtccaggaaatttaacccttccctcctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCC

Basic information

species Oryza sativa
transcript LOC_Os06g01700.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G154278_T01 (Zea mays), 3'ss of exon 1
--aaaagttacgattctctctcaaatgatgtgatcattgtagaaatatgcatctttgtccaacatatgtccaggaaatttaacccttccctcctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCC
    ||| ||    | |||     |||  |   |  |  |   |||||      ||||      |   ||||  |      |   || || | | ||| ||| ||||| || ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||| | ||||||||||| || ||||| ||||||
ggttaagatatatatttctgctggatg-cgcatttttgttgcgaatatatcaggttgtggtttgtccctccataactcactatttttgcc-catgtgtacagAAAAGACGGTCAACAGACCCAAGAGGAGTTACAGAAGAGGAATCTCAGGGAGGAACTTGAGGAACGTGAGCGCAAGCACTACTCTTCCAAGGATAAGTCC

upper sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G062076_T01 (Zea mays), 3'ss of exon 1
aaaagttacgat-tctctctcaaatga-tgtgatcattgtagaaatatgcatctttgtccaacatatgtccaggaa-atttaacccttccctccta--tgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCC
 |  |||| ||| | | | ||   ||  |||| |  |||| |  |     || |  | |  |  | |||||    | |  | ||  ||    || |  ||| ||| ||||| || ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||| | ||||||||||| || ||||| ||||  
catggttaagatatatatttctgctggctgtgttttttgttgcga---atatgtcaggctgaggtttgtccttccataactcactgtttttgcccacgtgtacAGAAAAGACGGTCAACAGACCCAAGAGGAGTTACAGAAGAGGAATCTCAGGGAGGAACTTGAGGAACGTGAGCGCAAGCACTACTCTTCCAAGGATAAGT--

upper sequence: LOC_Os06g01700.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G062076_T02 (Zea mays), 3'ss of exon 1
aaaagttacgat-tctctctcaaatga-tgtgatcattgtagaaatatgcatctttgtccaacatatgtccaggaa-atttaacccttccctccta--tgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCC
    |||| ||| | | | ||   ||  |||| |  |||| |  |     || |  | |  |  | |||||    | |  | ||  ||    || |  ||| ||| ||||| || ||||| |||||||| |||||||||||||||||||||||||| ||||||||||| |||||| | ||||||||||| || ||||| ||||||
--tggttaagatatatatttctgctggctgtgttttttgttgcga---atatgtcaggctgaggtttgtccttccataactcactgtttttgcccacgtgtacagAAAAGACGGTCAACAGACCCAAGAGGAGTTACAGAAGAGGAATCTCAGGGAGGAACTTGAGGAACGTGAGCGCAAGCACTACTCTTCCAAGGATAAGTCC

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|88420938|gb|CI620256.1|CI620256
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88402391|gb|CI596252.1|CI596252
EST:     CAGAAGTACTCCTCCCGCGACTTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|86831590|gb|CI301440.1|CI301440
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88573290|gb|CI664861.1|CI664861
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88742245|gb|CI765753.1|CI765753
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88427649|gb|CI689512.1|CI689512
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|86904323|gb|CI306741.1|CI306741
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCNAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88444118|gb|CI594491.1|CI594491
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAATATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88743536|gb|CI767044.1|CI767044
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88301238|gb|CI594764.1|CI594764
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88402420|gb|CI596281.1|CI596281
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88377322|gb|CI600477.1|CI600477
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88339685|gb|CI660475.1|CI660475
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|218478277|gb|FG948227.1|FG948227
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCCGGTA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
EST: gi|88342051|gb|CI644388.1|CI644388
EST:     CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAG                         GAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA
genomic: CAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGA

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: 64 (upstream exon), 71 (downstream exon)
Score: 178

CGGCCAAGGGCGGCAACGAGCAGGGCGGCACCCGCATCTTCGGGCCCTCGCAGAAGTACTCCTCCCGCGACCTCGCCGCCCACACCACCCTCAAGCCCAGgtactctttc ... ctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatctttgtccaacatatgtccaggaaatttaacccttccctcctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCC
                             atttaac  putative branch site (score: 178)
                                   cccttccctcctatgt  CT-rich tract
                           aaatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagttacgattctctctcaaatgatgtgatcattgtagaaatatgcatctttgtccaacatatgtccaggaaatttaacccttccctcctatgtccagGAAAGAAGGACAACATACCCAAGAAGAGTTACAGAAGAGGAATCTCAGGGACGAACTTGAGGAGCGTGAGAGGAAGCACTACTCGTCAAAGGACAAGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - atgatgt
- - - - - - - - - - - - - - - - - - - - - - atgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacata