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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctgaatccactaaaaccatgagcaagagcaacaaaaacctgtatatatacttgtttgcttactgtatgccattgctttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 4
GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctgaatccactaaaaccatgagcaagagcaacaaaaacctgtatatatacttgtttgcttactgtatgccattgctttgcag---------------
|||||||||||||||||||||||||||| |||||||||||| |  || |            ||  |       |   | | ||| |||||       || |   || |  | | |||  |                
GAGCCACCCAGAACTCTATCAGGGTTGCCCAAgtaagctctcaggcctc---gtttggagacagtatttctggactaccggataaatact-acacttttgcaaaatactctggttttcaaaagcttctgggtgttt

upper sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 4
GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctgaatccactaaaaccatgagcaagagcaacaaaaacctgtatatatacttgtttgctt-actgtatgccattgctttgcag-------------
|||||||||||||||||||||||||||| |||||||||||| |  |  ||        ||  |||  |  |   ||  |  | ||| | |   | | ||  |   || |  | | |||| |              
GAGCCACCCAGAACTCTATCAGGGTTGCCCAAgtaagctcttaggc--ctcgtttggagacaaagtacttctggaatat-caaataaattctatggttttgcaaaatactctggttttgaaaagcttatgggtgt
















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|84117280|gb|CD151047.1|CD151047
EST:     GAGCCACCCCCAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|27576661|gb|CA999355.1|CA999355
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|428330|gb|D24478.1|D24478
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGG
EST: gi|58598930|gb|CK009458.1|CK009458
EST:     GAGCCACCCAGAACTCTATCCGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|163918496|gb|EG710298.1|EG710298
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|428228|gb|D24376.1|D24376
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|88719065|gb|CI742575.1|CI742575
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|88733084|gb|CI756261.1|CI756261
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAG
EST: gi|88394239|gb|CI603428.1|CI603428
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|55410432|gb|CV722808.1|CV722808
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|58657974|gb|CK046654.1|CK046654
EST:     GAGCCACCCAGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
EST: gi|2311475|gb|C27630.1|C27630
EST:     AGAACTCTATCAGGGTTGCTCAA                         TGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG
genomic: AGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAG

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: 67 (upstream exon), 71 (downstream exon)
Score: 75

GAGCCACCCAGAACTCTATCAGGGTTGCTCAAgtaagctctg ... tgctttgcagTGGATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTA




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