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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgcggcccacgattcatggggttcttggttttcttggaatgttcaggaaatcttgttttctttttcctttgatggttggggtgttgttgcagCTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGGCTGGGTGGTCGGCCGGCGGCGGCGGCGACCCTTGCGGCGCGGGGTGGCA

Basic information

species Oryza sativa
transcript LOC_Os02g09740.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09740.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G103070_T02 (Zea mays), 3'ss of exon 1
---------gtgagctgcggcccacgattca--tggggttcttggttttcttggaatgttcaggaaatcttg-ttttctttttccttt-----------gatggttggggtgt-tgttgcagCTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGGCTGGGTGGTCGGCCGGCGGCGGCGGCGACCCTTGCGGCGCGGGGTGGCA---
          || || |||  ||  | | |   || | ||||||||||  | |||  |    |    | ||  |||||||| |  |||           ||||||| || |   ||||||||| |||||||| | |||||| ||  | || |||||||||||||||||||||||||||||||||||| |||||||||   | || |||||||||| ||||||   
gtaagagccctgggcggcgctcccggttccggctgagtttcttggtttcttgggatggcgtggtgggttttccttttctttcttgtttcgcgcgcgattgatggttcggttccgtgttgcagCCGCGGCGCTGGCGAATCTCTACACCTCCTGGAACAGCCCGTCGCAGCTGGCTGGGTGGTCGGCCAGCGGCGGCG---ATCCCTGCGGCGCGGCGTGGCAGGG
















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|88360457|gb|CI608459.1|CI608459
EST:     TCTTGCTGTCTCGTCGGCGCCGGCGGGAGC-ACCACCGACGCCTCCGAGG                         CTGCGGCGCTTGGGAATCTGTA
genomic: TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACGgtgagctgcg ... gttgttgcagCTGCGGCGCTTGGGAATCTGTA
EST: gi|88310800|gb|CI659403.1|CI659403
EST:     TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACG                         CTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG
genomic: TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACGgtgagctgcg ... gttgttgcagCTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG
EST: gi|88721234|gb|CI744533.1|CI744533
EST:     TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACG                         CTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG
genomic: TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACGgtgagctgcg ... gttgttgcagCTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG
EST: gi|88575273|gb|CI669418.1|CI669418
EST:     TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACG                         CTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG
genomic: TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACGgtgagctgcg ... gttgttgcagCTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG
EST: gi|88726154|gb|CI749809.1|CI749809
EST:     TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACG                         CTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG
genomic: TCTTGCTGTCTCGTCGGCGCCGGCGGGAGCCACCACCGACGCCTCCGACGgtgagctgcg ... gttgttgcagCTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgttcaggaaatcttgttttctttttcctttgatggttggggtgttgttgcagCTGCGGCGCTTGGGAATCTGTATTCGTCGTGGAACAGCCCGTCGCAGCTGGCTGGGTGGTCGGCCGGCGGCGGCGGCGACCCTTGCGGCGCGGGGTGGCA
                             ctttgat  putative branch site (score: 5)
                  ttttcttttt  TA-rich tract