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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCAGGTACCTCGCAGAGAAGACTAATACTACTAAACCCGGCCGTGGAAAATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagttgtcccatggactgttttttttattggttactttcattctgtcatgtagacttaagcctataatgttttccaacaaaaacagtataatttt...

Basic information

species Oryza sativa
transcript LOC_Os12g03060.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03060.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G017941_T01 (Zea mays), 5'ss of exon 8
AGGCAGGTACCTCGCAGAGAAGACTAATACTACTAAACCCGGCCGT---GGAAAATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagttgtcc-catggactgtttttt-ttattggttactttcattctgtcatgtagacttaagcctataatgttttccaacaaaaacagtataatttt-------------------------------------------------------
      | |||| || |||| ||||||   ||| ||| | ||||      | |||||||| || |||||| |||| ||||||||||| || ||||||| |||||| |||||| ||   | ||  || | |||  ||  | |||  ||  ||||||  | || | |||  || |  |  |   |      ||| |  | | |  ||                                                       
------GCACCTTGCGGAGAGGACTAACGGTACAAAAACTGGCCTACTGAGCAAATGTGACGGAGAGTGCCTAGTCAAATCAACTCTTCTTGAAGGAACCTTTGTCgtaagtcgtttacctgtgctctgtttcattgctcgttggttctattctga-acgtgggctt--gcatgcaggggggtggggggaaatccatgttacgttgtcagtgtgccttgtatccttgtgttgtattctcacgcttgtctactatgtgcag
















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|29657294|gb|CB653569.1|CB653569
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88239235|gb|CI240397.1|CI240397
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|33653555|gb|CF276169.1|CF276169
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|29687248|gb|CB683523.1|CB683523
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTTTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88416649|gb|CI543550.1|CI543550
EST:     TGCTAGAAGGAAGCTTTGTT                       
genomic: TGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|163926921|gb|EG715146.1|EG715146
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88906025|gb|CI089611.1|CI089611
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|88384390|gb|CI551316.1|CI551316
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|38478567|gb|CF962700.1|CF962700
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCACATGTATGATGGGA
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGGA
EST: gi|86598271|gb|CI354888.1|CI354888
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|87028733|gb|CI349452.1|CI349452
EST:     TGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: TGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|33805224|gb|CF328489.1|CF328489
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|38471525|gb|CF955656.1|CF955656
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|29618675|gb|CB623687.1|CB623687
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|88446415|gb|CI563245.1|CI563245
EST:     TTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: TTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|58694491|gb|CK083178.1|CK083178
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|86834645|gb|CI340762.1|CI340762
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|58674334|gb|CK063020.1|CK063020
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|86831384|gb|CI299442.1|CI299442
EST:     AATGTGATGGGGAGTGCTTAGTACAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATA
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATA
EST: gi|88278361|gb|CI399361.1|CI399361
EST:     TAGAAGGAAGCTTTGTT                       
genomic: TAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|88291767|gb|CI539938.1|CI539938
EST:     GGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: GGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|88995219|gb|CI036794.1|CI036794
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCNACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|38475562|gb|CF959695.1|CF959695
EST:     GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTGTGTT                         GGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGG
genomic: GTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgcagGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATGGG
EST: gi|88278276|gb|CI399276.1|CI399276
EST:     GCTAGAAGGAAGCTTTGTT                       
genomic: GCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|89178438|gb|CI015143.1|CI015143
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc
EST: gi|33681633|gb|CF309872.1|CF309872
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTT                         GTTGGAATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagtt ... tgatatgcagG--G-AATAGTGCTGCTAATCATCTTGATATCAGGACTCAAATGTATGATG
EST: gi|86418859|gb|CI053660.1|CI053660
EST:     AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTGTT                       
genomic: AATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGC--T-TTgttgtaagtt ... tgatatgc

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCAGGTACCTCGCAGAGAAGACTAATACTACTAAACCCGGCCGTGGAAAATGTGATGGGGAGTGCTTAGTAAAATCAACTCTGCTAGAAGGAAGCTTTgttgtaagttgtcccatggactgttttttttattggttactttcattctgtcatgtagacttaagcctataatgttttccaacaaaaacagtataatttt

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaaa