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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCGTCGAGCACTACGCTAATGCCTATGTCTTCACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcctcttattattattagtattactagtctagccagtactgtgcctctctgctcaaagcatcaaacgatatgctgcatagattgaattttcgct...

Basic information

species Oryza sativa
transcript LOC_Os12g01430.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G155437_T01 (Zea mays), 5'ss of exon 2
ATGCCGTCGAGCACTACGCTAATGCCTATGTCTTCACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcctcttattattattagtattactagtctagccagtactgtgcctctctgctcaaagcatc-aaacgatatgctgcatagattgaattttcgct
||||||| ||  | |||   |  |||||||| || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || |||||| |     | |  |||   ||   | ||  |    |   | |   ||  |   ||      |  | || || | ||||  | |   | |  |         
ATGCCGTGGACAAGTACAGCAGCGCCTATGTTTTTACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCTAGCAGgcacggcgcccacattgc-atgtctgttgattccgtcttctgctttggtcaaatccatcttacccttccaagcaatatttttc--tgttccag--------

upper sequence: LOC_Os12g01430.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G467086_T01 (Zea mays), 5'ss of exon 2
ATGCCGTCGAGCACTACGCTAATGCCTATGTCTTCACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgta-gctgcct------cttattattattagtattactagtctagccagtactgtg---------------cctctctgctcaaagcatcaaacgatatgctgcatagattgaattttcgct---
|||| |||||  | |||   |  |||||||| || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || |||||||| |  |||       | |  | ||  |  | |  |    |    ||||   |||               |   ||||||     |||| | |       | |||  | |   || |       
ATGCTGTCGACAAATACAGCAGCGCCTATGTTTTTACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGGGAGCAGCTCAAGTCTTCGAGCAGgtacggcgcccacattgcatgctgttgattctgtctccgaacgctgcagtggagtggaccggatctaattccgcttctgctttggtcatccatcttacccttccatgcaatatgttctgttccag
















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|33798312|gb|CF325013.1|CF325013
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCATC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|33822729|gb|CF337172.1|CF337172
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCATC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88728599|gb|CI752109.1|CI752109
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88296130|gb|CI667520.1|CI667520
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|33686639|gb|CF314878.1|CF314878
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGANTAGCGTTGGGGCGTTCAC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGA-TAGCGTTGGGGCGTTCAC
EST: gi|163918505|gb|EG711435.1|EG711435
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|33798269|gb|CF324991.1|CF324991
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCATC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88342605|gb|CI656127.1|CI656127
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCATC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|55440809|gb|CV733716.1|CV733716
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCATC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88454180|gb|CI694474.1|CI694474
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCATC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88722956|gb|CI746466.1|CI746466
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGT
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGT
EST: gi|88347469|gb|CI637409.1|CI637409
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|218490970|gb|FG950243.1|FG950243
EST:     GGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCACAGC-G                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCAC
genomic: GGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTC-CAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCAC
EST: gi|163925538|gb|EG713379.1|EG713379
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88302253|gb|CI668099.1|CI668099
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88302497|gb|CI668343.1|CI668343
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88294157|gb|CI667131.1|CI667131
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|218498120|gb|FG965520.1|FG965520
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGCTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
EST: gi|88301855|gb|CI667701.1|CI667701
EST:     AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAG                         GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC
genomic: AGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcct ... tttatgtcagGATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCGTCGAGCACTACGCTAATGCCTATGTCTTCACCTACGATAACATGAGGAATCAGAAGCTCAAGGACCTCAGAGAGCAGCTCAAGTCCTCCAGCAGgtagctgcctcttattattattagtattactagtctagccagtactgtgcctctctgctcaaagcatcaaacgatatgctgcatagattgaattttcgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA