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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT

Basic information

species Oryza sativa
transcript LOC_Os03g38590.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G124918_T01 (Zea mays), 3'ss of exon 12
gtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT-
          || ||  | |  |   | |  |||||     | |   |   |||  |   ||  |  ||        ||| | ||  | ||   ||  |  |    |||||||||||| || || |||||||| || || ||||| || || ||||||| ||| || || |||||||| || |||||||| || |||||| ||    ||  || 
----------gtgtgaagttactaaatat--gttgctctcctattc-atctcttgacaccttcaattggt-------tctgaactgttaagttttgc-caacacctactgcagCGTGTTTACCTCTACTTCCGAGGAAGTGGGAAGGAAGCGGAGATGAGGCGGGAAGCAGCACGCAGTGCTGCGAGGGCAGCATTTTGACGA-ACCGTGTGTG

upper sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G011078_T02 (Zea mays), 3'ss of exon 11
gtcaagtcctgtctgctgctggttcttttctgttgcctgaatttctgaatgcttagcgtttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGAT-GTACGT
          ||    |  |   |   | | | | | |  || |||   | |||  |   ||         | ||  |       ||| |   || |||  ||||||     ||| || || || |||||||| || ||||||||||| || ||||||| ||| || || |||||| | ||||||||||| ||||||||||||  |  |||   
----------gtgaagttattactgcctaccgcttcattgatctctc--ttcttgacaccttc--------agttggttctgaactgtaaaagctctgcatcctgca-----gCGCGTCTACCTGTACTTCCGAGGGAGCGGGAAAGAAGCGGAGATGAGGCGTGAAGCAGCACGCGGTGCAGCGAGGGCAGCGTTTTGATGAAAACCGTATA-
















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|12404727|gb|AU166328.1|AU166328
EST:     GTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88506206|gb|CI433712.1|CI433712
EST:     CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88475023|gb|CI412294.1|CI412294
EST:     ATTCGCAATG-TTTGCCTGGGAGTCCCTGGTCAGCATGTGGGTTATTCAG                         CGTGGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
genomic: ATTCGCAATGTTTTGCCT-GGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGT-GTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
EST: gi|88258581|gb|CI361167.1|CI361167
EST:     TGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTTTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATTAAGCGC
genomic: TGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88476593|gb|CI413864.1|CI413864
EST:     TCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: TCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88428152|gb|CI557046.1|CI557046
EST:     TGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: TGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88482190|gb|CI419461.1|CI419461
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88511461|gb|CI438967.1|CI438967
EST:     GATTCCCAATNTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCC-GGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
EST: gi|29662769|gb|CB659044.1|CB659044
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGGGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCG
EST: gi|86884619|gb|CI312998.1|CI312998
EST:     ATTCCCAATGTTTTGCCTGGAATCGCTGCTCAGGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: ATTCGCAATGTTTTGCCTGGAGTCGCTGCTCA-GCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88260970|gb|CI364546.1|CI364546
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCACCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|29662682|gb|CB658957.1|CB658957
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|86511240|gb|CI153873.1|CI153873
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|29662718|gb|CB658993.1|CB658993
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88366315|gb|CI553713.1|CI553713
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88485149|gb|CI422420.1|CI422420
EST:     GATTCGCAATGTTTTGCCTGGATTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCACCGGGAAAGAGGCCGAGATGAAGCCC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|86261561|gb|CI017303.1|CI017303
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88509345|gb|CI436851.1|CI436851
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88475024|gb|CI412295.1|CI412295
EST:     GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: GATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC
EST: gi|88284372|gb|CI405818.1|CI405818
EST:     CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATNTGGGTTATTCAG                         CGTGTGTATCTTTACTTCCGGGCCAGCGGGAAAGAGGCCGAGATGAAGCGC
genomic: CGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGC

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: 66 (upstream exon), 67 (downstream exon)
Score: 11

GTGTTTTATTTTCTTGGATTCGCAATGTTTTGCCTGGAGTCGCTGCTCAGCATGTGGGTTATTCAGgtcaagtcct ... tgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcagaggaaaatttatctaaccttgtgagcactgtgctccctgcactgcagCGTGTGTATCTTTACTTCCGGGGCAGCGGGAAAGAGGCCGAGATGAAGCGCGAGGCTGCACGCAGCGCAGCGAGGGCGGCGTTTTGATGATGATGTACGT
                  atctaac  putative branch site (score: 11)
                                      tgctccct  putative PPT
           aaaatttatctaa  TA-rich tract