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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgactagaacctttatgatttaaatcatttgtggtaaatcacaattcagatgctttgcagacgttctgagctgccctcatgttcgtttttcttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTCCTCGACAAAGACCGCCCTTTCTTCCCTCCAACAATCAACAGCGCGGGGC

Basic information

species Oryza sativa
transcript LOC_Os01g37960.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g37960.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G090779_T01 (Zea mays), 3'ss of exon 4
tgactagaacctttatgatttaaatcatttgtggtaaatcacaattcaga-tgctttgcagacg---ttctgagctgccctca------tgttc-gtttttcttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTCCTCGACAAAGACCGCCCTTTCTTCCCTCCAACAATCAACAGCGCGGGGC
         | | | |||  | |  || || |  | | |  || |   || ||   |||||| |    |  |||  | |||||      |  || |||| || ||| |||||| |||||||| |||||   ||||||||| ||||  |||| ||| |||||||||  ||| ||||| ||||||||||| || || ||||||||| | | ||
---------cttctctgaagtcacgcaatttt--ttagtttcagtgtggactgtcgtgcagaggagactgcgagtggacctcagtaagctactctgtttctcatgtctcagGTGATTGTGTCTCAAGCTAGCGTGCAGCGCTGCAGCGCTGCCGTGGACTTCCTCAGCAAGGACCGTCCTTTCTTCCCGCCGACCATCAACAGCCCCGAGC
















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|58688291|gb|CK076978.1|CK076978
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|86823459|gb|CI256413.1|CI256413
EST:     CAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: CAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|58587717|gb|CF986025.1|CF986025
EST:     AGCCTTTTTAAAAGGGGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: AGCCTTTTTAAAA-GAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|426822|gb|D22895.1|D22895
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATTNCTGTCGTAG-CT
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagG-TCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATG-CTGTCGTAGACT
EST: gi|38477599|gb|CF961732.1|CF961732
EST:     GAGCCGTGGTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|58681864|gb|CK070551.1|CK070551
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGACGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|218497348|gb|FG955372.1|FG955372
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|58590412|gb|CF988720.1|CF988720
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|58588534|gb|CF986842.1|CF986842
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|86496037|gb|CI138670.1|CI138670
EST:     GACCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|25778006|gb|CA752758.1|CA752758
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|38473362|gb|CF957494.1|CF957494
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|163921031|gb|EG710131.1|EG710131
EST:     AGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: AGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAG-CAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|58588306|gb|CF986614.1|CF986614
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
EST: gi|58684058|gb|CK072745.1|CK072745
EST:     GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAG                         GTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC
genomic: GAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTC

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), 75 (downstream exon)
Score: 31

TGGAGCCTTCAATGTCATCCCTGATTCTGTTACAATTGGTGGCACCTTCCGAGCCTTTTTAAAAGAGAGTTTTAATCAATTGAAGCAGCGAATTGAAGAGgtaactgcaa ... cttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTCCTCGACAAAGACCGCCCTTTCTTCCCTCCAACAATCAACAGCGCGGGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatgctttgcagacgttctgagctgccctcatgttcgtttttcttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTCCTCGACAAAGACCGCCCTTTCTTCCCTCCAACAATCAACAGCGCGGGGC
                                  tgttcgtttttctt  CT-rich tract
                                        tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgactagaacctttatgatttaaatcatttgtggtaaatcacaattcagatgctttgcagacgttctgagctgccctcatgttcgtttttcttgtgtcagGTCATTGTGTCACAAGCATCCGTGCAGCGGTGCAATGCTGTCGTAGACTTCCTCGACAAAGACCGCCCTTTCTTCCCTCCAACAATCAACAGCGCGGGGC

- - - - - - ttatgat
- - - - - - - - - - - - tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - ctttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctgcc