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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttaagaagagtagtcacacacaatatctttttatcaaggtatattcttataagaagttttcaacaagatttgcttgaaaatttgagtctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTC

Basic information

species Oryza sativa
transcript LOC_Os02g10180.2
intron # 1
splice site 3'
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|88360289|gb|CI612008.1|CI612008
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         --G-CAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88719860|gb|CI741795.1|CI741795
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         --G-CAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGG
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGG
EST: gi|88421491|gb|CI618615.1|CI618615
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCAACGAATCGTCGCTCGCCG                         --G-CAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88694893|gb|CI738931.1|CI738931
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         CAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88407064|gb|CI581151.1|CI581151
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         CAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|58679386|gb|CK068073.1|CK068073
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         CAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88397149|gb|CI593361.1|CI593361
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         CAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88390899|gb|CI611125.1|CI611125
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         --G-CAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88731190|gb|CI754803.1|CI754803
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         CAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88417075|gb|CI573790.1|CI573790
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         --G-CAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|58664588|gb|CK053274.1|CK053274
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCG-C-                         C-GGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88315839|gb|CI617312.1|CI617312
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         CAGGCAGAAATAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88725664|gb|CI748923.1|CI748923
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         --G-CAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|58694698|gb|CK083385.1|CK083385
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         CAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
EST: gi|88396806|gb|CI620139.1|CI620139
EST:     CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCG                         --G-CAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT
genomic: CAGAGGTGGCGCCCGGCGTCCTCCTGCTTCCACCGCATCGTCGCTCGCCGgtgagcatcc ... tctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttataagaagttttcaacaagatttgcttgaaaatttgagtctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTC
                                            gtctaat  putative branch site (score: 3)
     ttataagaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttaagaagagtagtcacacacaatatctttttatcaaggtatattcttataagaagttttcaacaagatttgcttgaaaatttgagtctaatttagCAGGCAGAACTAAGAGAGCATGGTGGCGATGGCGCGGTGGCCGTGGAGGGTGCTGCTGCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - aagaagag
- - - - - - - - - -acacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - ataagaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcttg