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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTATTCGTTGGTAATGTACCCAAGGGGTTGGGTGAGGAGGAGCTGAGAAAGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttttgatttcacagttgtattttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcag

Basic information

species Oryza sativa
transcript LOC_Os11g14430.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g14430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G103430_T04 (Zea mays), 5'ss of exon 4
GCTATTCGTTGGTAATGTACCCAAGGGGTTGGGTGAGGAGGAGCTGAGAAAGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcag---
||| || ||||| ||||| ||||||||| || | ||||||||||| |  || |  ||| | |||||||| ||||||||| |||||||||||||||| ||||||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |  | | |    
GCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgcacaggatcag

upper sequence: LOC_Os11g14430.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G103430_T05 (Zea mays), 5'ss of exon 3
GCTATTCGTTGGTAATGTACCCAAGGGGTTGGGTGAGGAGGAGCTGAGAAAGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttttgatttcacagttgtatt---ttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcag
||| || ||||| ||||| ||||||||| || | ||||||||||| |  || |  ||| | |||||||| ||||||||| |||||||||||||||| ||||||||  || || ||||    |||| ||   ||||||  || | || |||  ||  ||||||  ||  | || || |  | |   
GCTGTTTGTTGGGAATGTGCCCAAGGGGCTGAGCGAGGAGGAGCTTACCAACACTATCAAGGGGAAGGGTCCAGGTGTTATCAACATTGAGATGTTTAAGgtgtgctttgtggtttcgtgcttgttttcgtttgtacaccacaagttccagattcactaatattgagatgctgtttgcacag---
















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|29639969|gb|CB644978.1|CB644978
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|218479912|gb|FG956819.1|FG956819
EST:     GTGTTGTCAACATTGAGA-G-TCAAG                         GGTTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: GTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|29664577|gb|CB660852.1|CB660852
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|58609361|gb|CK037394.1|CK037394
EST:     AGATAATCCAGGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|58693279|gb|CK081966.1|CK081966
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|29640012|gb|CB645021.1|CB645021
EST:     AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: AGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
EST: gi|38473107|gb|CF957239.1|CF957239
EST:     GGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAG                         GATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT
genomic: GGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttt ... ggtcctgcagGATTTACATGACCCAAGCCGTAACCGTGGGTTCCTCTTTGTTGAGTATTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTATTCGTTGGTAATGTACCCAAGGGGTTGGGTGAGGAGGAGCTGAGAAAGATAATCCAAGGGAAGGGGCCAGGTGTTGTCAACATTGAGATGTTCAAGgtgtgtcttttgatttcacagttgtattttgtacgacaaaggtcccaagtttgctaatagagatgttctcttggtcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG