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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtattttaccagttgttcaagattatgcattttctttcttacccatatgtattttttttccag

Basic information

species Oryza sativa
transcript LOC_Os11g40510.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 6
GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtattttaccagttgttcaagattatgcattttctttcttacccatatgtattttttttccag
| |||||||||||||||||||| ||||||||||||||||| || |||||| |||||||||| |||||| ||||||   | | |||||||||||   | |  |  |||     | | |  |   |  | || ||| | |         ||||||||| | ||  ||  |  |||  || |    | || |    | |  || |      |  |   |   |||| |||
GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGATACTCTACTTGCTCgtaagcactgcctggctct---catctctcctccatttacttgtcattgt--------tgacattttagcagagtggcttgctacttgt-gcagtacatgacatgtctatttaccagtttagcttggtaacttttgcag

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 7
GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtattttaccagttgttcaagattatgcattttctttcttacccatatgtattttttttccag
| |||||||||||||||||||| ||||||||||||||||| || |||||| |||||||||| |||||| |||| |   | | |||||||||||   | |  |  |||     | | |  |   |  | || ||| | |         ||||||||| | ||  ||  |  |||  || |    | || |    | |  || ||     |  |   |   |||| |||
GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTCgtaagcactgcctggctct---catctctcctccatttacttgtcattgt--------tgacattttagcagagtggcttgctacttgt-gcagtacatgacatgtctatttactagtttagcttggtaacttttgcag
















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|58688359|gb|CK077046.1|CK077046
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|86897973|gb|CI290697.1|CI290697
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAG
EST: gi|87012285|gb|CI293335.1|CI293335
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGAT
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGAT
EST: gi|58687280|gb|CK075967.1|CK075967
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|87006051|gb|CI289468.1|CI289468
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58602505|gb|CK013033.1|CK013033
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|33680119|gb|CF308358.1|CF308358
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58681227|gb|CK069914.1|CK069914
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGAT
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGAT
EST: gi|88572117|gb|CI663688.1|CI663688
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|86905007|gb|CI289154.1|CI289154
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|88321854|gb|CI672999.1|CI672999
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCACAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58678674|gb|CK067361.1|CK067361
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58690866|gb|CK079553.1|CK079553
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|87022688|gb|CI293578.1|CI293578
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTNGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58694246|gb|CK082933.1|CK082933
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|25797088|gb|CA753049.1|CA753049
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|218500911|gb|FG960833.1|FG960833
EST:     GTAACAGATGCTGCATTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58597389|gb|CK007917.1|CK007917
EST:     TAACAGATGCTGCTTTGTTGTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: TAACAGATGCTGCTTTGTT-TGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58606512|gb|CK034545.1|CK034545
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|58601763|gb|CK012291.1|CK012291
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTAGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|86596642|gb|CI286555.1|CI286555
EST:     GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: GTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
EST: gi|87004665|gb|CI300987.1|CI300987
EST:     CAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC                         AGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG
genomic: CAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgttt ... ttttttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTCgtaagtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtattttaccagttgttcaagattatgcattttctttcttacccatatgtattttttttccag

- - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA