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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCGATGCTGCTTTGGCCTATCTCAGTAGCCAGTGCAAGAACCTGAAATGCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagtagttgcgccattgctctccatcgaattctttctgatctttataaccttgatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g65920.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65920.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G138176_T01 (Zea mays), 5'ss of exon 3
CAGCGATGCTGCTTTGGCCTATCTCAGTAGCCAGTGCAAGAACCTGAAATGCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagta-gttgcgccattgctctccatcgaattctttctgatctttataaccttgatgcag-----------------
|||||| |  ||  | |  |  |||   |||||||||  |||||||| ||||||||| |||||||||||||||||||| |  || ||||||||  | |||||||    ||  | |||  | ||| || |  | ||  ||    |||||  |      ||| ||  |                 
CAGCGACGTGGCGCTCGTGTTCCTCTCCAGCCAGTGCGGGAACCTGAGATGCCTGAACCTGTGCGGGTGTGTGAGGGCGGCCTCTGACAGAGCGCTACAGgtactttcgtttgctgcagccttggtcgc--ttgagctcgcgttgatccctgctgttttggtggtgtgtcctgtcctgtgtag
















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|1631760|gb|C19489.1|C19489
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTNGTGT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
EST: gi|4880775|gb|AU065074.1|AU065074
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
EST: gi|218481897|gb|FG957216.1|FG957216
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATT----                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
EST: gi|29646357|gb|CB651364.1|CB651364
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
EST: gi|5003534|gb|AU068683.1|AU068683
EST:     TGTGCGGGTNTTTGAGGGCAGTTTCCGAACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
genomic: TGTGCGGGTGTGTGAGGGCAGTTTCCG-ACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
EST: gi|4880754|gb|AU065053.1|AU065053
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
EST: gi|29643872|gb|CB648879.1|CB648879
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
EST: gi|29643871|gb|CB648878.1|CB648878
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCT
EST: gi|218478607|gb|FG965535.1|FG965535
EST:     GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAG                         GCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT
genomic: GCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagt ... cttgatgcagGCCATCGCCTGTAACTGTGGTCAGCTTCAGTCTTTGAACCTAGGCTGGTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCGATGCTGCTTTGGCCTATCTCAGTAGCCAGTGCAAGAACCTGAAATGCCTGAATCTGTGCGGGTGTGTGAGGGCAGTTTCCGACAGAGCATTGCAGgtaccaaagtagttgcgccattgctctccatcgaattctttctgatctttataaccttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA