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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAAGTACCGGAAGGCCATCCTCTACCTGGTGGAGCGGCACGCCACGACCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttctaggcgtatgaatggctctcggtttcccattgcagttgccactgggacgattttcttggtgtgcggagagatctgtccgaggcatttggt...

Basic information

species Oryza sativa
transcript LOC_Os01g11370.1
intron # 2
splice site 5'
intron type U2

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|29625175|gb|CB630186.1|CB630186
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88362444|gb|CI623784.1|CI623784
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88356674|gb|CI619160.1|CI619160
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGC
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGC
EST: gi|88388923|gb|CI592811.1|CI592811
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|58691453|gb|CK080140.1|CK080140
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|29658869|gb|CB655144.1|CB655144
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88312143|gb|CI580308.1|CI580308
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATACCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGAATTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88411265|gb|CI564386.1|CI564386
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88727156|gb|CI750811.1|CI750811
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88366515|gb|CI610734.1|CI610734
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|58674693|gb|CK063380.1|CK063380
EST:     GGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: GGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88730378|gb|CI753991.1|CI753991
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCT
EST: gi|29626953|gb|CB631964.1|CB631964
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|29636300|gb|CB641309.1|CB641309
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88441713|gb|CI599618.1|CI599618
EST:     ACATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|29624813|gb|CB629824.1|CB629824
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88324258|gb|CI566071.1|CI566071
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88726049|gb|CI749704.1|CI749704
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCA
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCA
EST: gi|88693453|gb|CI737028.1|CI737028
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88430331|gb|CI567350.1|CI567350
EST:     CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
EST: gi|88430530|gb|CI569553.1|CI569553
EST:     CCATCGTCGTCGGCGAGAC-GGCAGCGGAAAGTCCACGCAGATCC-TCAG                         TACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT
genomic: CCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACT

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: 63 (upstream exon), 55 (downstream exon)
Score: 8

GTACAAGTACCGGAAGGCCATCCTCTACCTGGTGGAGCGGCACGCCACGACCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttc ... cttttatcagTACCTTAAAGAGGCTGGATGGGCCGAGGGTGGTCGACTTATAGGCTGCACTCAACCAAGACGATTGGCCGTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAAGTACCGGAAGGCCATCCTCTACCTGGTGGAGCGGCACGCCACGACCATCGTCGTCGGCGAGACCGGCAGCGGAAAGTCCACGCAGATCCCTCAGgtatgtgttctaggcgtatgaatggctctcggtttcccattgcagttgccactgggacgattttcttggtgtgcggagagatctgtccgaggcatttggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT