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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctactacttatccttgtgtactgcctttcatccatgcgctcctatttgtggtgctctcgacgactgacttttatcatgtactgtaatacttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATATGCACGGTTCTAATTTGAAGAGCACACTCACAGGATATATGCACTATCCA

Basic information

species Oryza sativa
transcript LOC_Os01g01420.3
intron # 7
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|89190252|gb|CI392302.1|CI392302
EST:     CCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCACTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: CCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88260697|gb|CI362990.1|CI362990
EST:     GTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|86597810|gb|CI276596.1|CI276596
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|23513969|gb|BU673403.1|BU673403
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88996416|gb|CI259920.1|CI259920
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|29628499|gb|CB633510.1|CB633510
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88531546|gb|CI460028.1|CI460028
EST:     AATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: AATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88560349|gb|CI491003.1|CI491003
EST:     AGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: AGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|89190253|gb|CI392303.1|CI392303
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCACTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88663803|gb|CI486749.1|CI486749
EST:     CTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: CTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88849918|gb|CI001624.1|CI001624
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88252353|gb|CI350781.1|CI350781
EST:     AGAATTTGAAGCTGGAATCTGGAGAGGCCACTCTTGAGCAGCGG                         CGTCTCTCGATTCTCGACTTTCTACAAAAACAATTGGATGACAGGTGATAT
genomic: AGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|89181635|gb|CI113141.1|CI113141
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|29637602|gb|CB642611.1|CB642611
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|86435733|gb|CI106966.1|CI106966
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|86864492|gb|CI334767.1|CI334767
EST:     GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: GCCTTGAGAATTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|86903234|gb|CI313597.1|CI313597
EST:     CCTTGAGAATTTTAAGGCTGGAATCTGGAGAGGCCAGTCTTGAGCACCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: CCTTGAGAATTTGAA-GCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
EST: gi|88509567|gb|CI437073.1|CI437073
EST:     TTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGG                         CGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT
genomic: TTTGAAGCTGGAATCTGGAGAGGCCAGTCTTGAGCAGCGGgtagctacta ... acttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttgtggtgctctcgacgactgacttttatcatgtactgtaatacttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATATGCACGGTTCTAATTTGAAGAGCACACTCACAGGATATATGCACTATCCA
                   gactgac  putative branch site (score: 2)
                                            tactttt  putative PPT
                                         taatactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctactacttatccttgtgtactgcctttcatccatgcgctcctatttgtggtgctctcgacgactgacttttatcatgtactgtaatacttttgcagCGTCTCTCGGTTCTCGACTTTCTACAAAAACAATTGGATGACAAGTGATATGCACGGTTCTAATTTGAAGAGCACACTCACAGGATATATGCACTATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA