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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactcaacctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccctacctgattgcatgtattctgtttcccgtgtcatcggtttcag

Basic information

species Oryza sativa
transcript LOC_Os05g38610.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G883149_T03 (Zea mays), 5'ss of exon 3
AAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactcaacctatttaatgtatctttgtttttctaccttttattttgttttacatttatgtccctac-ctgattgcatgt-attctgtttcccgtgtcatcggtttcag
||||||| || |||||||||||||||||||| |||||||||||||||||||||||||| || ||||| |||||| ||||||| || ||     |||||| |||||  ||   ||||| || || | | | ||   | |   ||| || ||||  |  ||  |||    |  ||||||| || | | | |||||||    |    ||||||||
AAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAGGAGAATGAGCTTATTTTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttatcttccctctattgaa-gtttatcttttcaaccattgtttgttctgttacatgttattgtgttaatgctgattgtatatgaatgtgtttccaaccttggtggtttcag

upper sequence: LOC_Os05g38610.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G431350_T01 (Zea mays), 5'ss of exon 3
AAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactcaacctatttaa-tgtatctttgtttttctaccttttattttgttttacatttatgtccctac-ctgattgcatgt-attctgtttcccgtgtcatcggtttcag
||||||| || |||||||||||||||||||| || ||||||||||||||||||||||| || ||||| |||||| ||||||| || ||     |||||| |||||  ||   ||||| || | ||||||||          |||| || ||||  |  ||  |||    |  ||||||| || | | | |||||||  | |    ||||||||
AAGACCTGCACTTTTTTGTTACTGGAGGAGAAGAAGAGAATGAGCTTATTTTAGCATCAGTTCTTCAGGGATTCTCTGATGCTGTCGAACGACTTCTCAAgttattttccctctattaaactttatctttgcaaccac-tgttttgttctgttacatgttgttgtgttaatgctgattgtatatgaatgtgtttccaatcttggtggtttcag
















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|58696220|gb|CK084907.1|CK084907
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|88983146|gb|CI020710.1|CI020710
EST:     TAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTGTCAGG                         AGATTACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
genomic: TAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCA-Ggttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
EST: gi|33688934|gb|CF317173.1|CF317173
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33692847|gb|CF321086.1|CF321086
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|396941400|gb|HO188609.1|HO188609
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33692848|gb|CF321087.1|CF321087
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|8857691|gb|AU095009.1|AU095009
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|29682909|gb|CB679184.1|CB679184
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33820855|gb|CF336232.1|CF336232
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33820857|gb|CF336233.1|CF336233
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGAACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCG-ACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTAT
EST: gi|163918457|gb|EG713211.1|EG713211
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33678548|gb|CF306787.1|CF306787
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|218504818|gb|FG952248.1|FG952248
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|218500698|gb|FG952590.1|FG952590
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|58585721|gb|CF984029.1|CF984029
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
EST: gi|33683273|gb|CF311512.1|CF311512
EST:     TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAG                         AAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT
genomic: TTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATT

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: 71 (upstream exon), 62 (downstream exon)
Score: 38

AAGACCTCCATTTTTTTGTTACTGGAGGAGAGGAGGAGAATGAGCTTATTTTAGCATCGGTCCTTCAAGGATTCACTGATGCAGTTGACATTATTCTCAGgttatactca ... tcggtttcagAAATAACGTCGACAAAAGAACAGCACTCGAAAATCTGGATCTCATCCTATTGTGCCTCGATGAAATTGTTGATGGAGG




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