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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGAGGGGGCTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgttatctgatgtagtcagtatgttcctcttagcattttcccctctttgccaagtgtcgctcataggtggtatcctcttgacactcgaattgtgctaactcatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g62080.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62080.2 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G386991_T01 (Zea mays), 5'ss of exon 11
TGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGAGGGGGCTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgttatctgatgtagtcagtatgttcctcttagcattttcccctctttgccaagtgtcg-ctcataggtggtatc-ctcttgaca---ctcgaattgtgctaactcatgcag
|||||||||||| ||||  || ||| |||||||||||||||||||||| || |||||||| || ||| |||||||||||||||||||||||||||||||||||||||  | ||||||||| ||    |  ||   |  ||||     |   || ||||| || |  ||  ||  ||||||  || |||| |    || |||  |   ||  |||||||
TGCTGAAAAGTACTTCAAGCGCGGAGTAAGGTTGGACTGGCCAGAGGGAGCGGCCTCACGAGAGAGCATGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttcctctctgatgtactc----taatcaattacgcat-----cagtttggccaactgacatcttttaaatggtatgacttttgaaaaagttctaatcattgcaatccatgcag
















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|27577533|gb|CB000228.1|CB000228
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|86419537|gb|CI054338.1|CI054338
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|88278121|gb|CI399121.1|CI399121
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|109712124|gb|CI104732.1|CI104732
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCT-
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|88268204|gb|CI378139.1|CI378139
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|88278123|gb|CI399123.1|CI399123
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|88902914|gb|CI088452.1|CI088452
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|86434684|gb|CI105917.1|CI105917
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|27576166|gb|CA998860.1|CA998860
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|86484027|gb|CI126660.1|CI126660
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
EST: gi|86598138|gb|CI278528.1|CI278528
EST:     CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAG                         AATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT
genomic: CTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgtt ... actcatgcagAATCTGGTAATGCAACATGTTGATCATTCTGCTGGAGATCTTATAGATCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGAAAAGTATTTCAGACGTGGATTAAGGTTGGACTGGCCAGAGGGGGCTGCCTCACGGGAAAGCCTGAAGGCAGTCTGGAAATTGCCTCGTCTGCAGgtactttgttatctgatgtagtcagtatgttcctcttagcattttcccctctttgccaagtgtcgctcataggtggtatcctcttgacactcgaattgtgctaactcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG