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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatcagagagtagtttttgtattaacttccatactagtttttcattatccagctaatttaaaaaccacaaggttctttactaatgttgtctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTCTTTGCAGTGCTTGATAGGCAACCCATGAAAATTTTCAGGGAAGAATGTG

Basic information

species Oryza sativa
transcript LOC_Os04g23890.3
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G032351_T01 (Zea mays), 3'ss of exon 13
acatcagagagtagtttttgtattaacttccatactagtttttcattatccagctaatttaaaaaccaca-aggttctttactaatgttgtctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTCTTTGCAGTGCTTGATAGGCAACCCATGAAAATTTTCAGGGAAGAATGTG
 ||  |  || || |     |  |   ||  ||     |  || ||| | ||  | | || ||    ||| |  | | | ||||||  |   | ||||||||| ||||||||||||||||||||||||||||||||||| ||||||||| | |||||| | || |||| |||||| |||||| ||||||| ||||||| ||
-cacaattgattattgaccttcatgttttgtatttccataatttattttgcattttacttgaatttaacatatatgcatcactaatcattgtttttttcagACACCAACACATGTTTGTCTCATAACAGACTTTTGTCCTGGAGGAGAATTATTTGCACTACTCGATATGCAACCAATGAAACTTTTCAGAGAAGAATCTG
















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|702138|gb|D48429.1|D48429
EST:     ACGCACTATTGGNTCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTNTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|33799059|gb|CF325389.1|CF325389
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|14571435|gb|BI118803.1|BI118803
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|58587914|gb|CF986222.1|CF986222
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAG
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAG
EST: gi|29615865|gb|CB620877.1|CB620877
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGA
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGA
EST: gi|29686409|gb|CB682684.1|CB682684
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
EST: gi|29646469|gb|CB651476.1|CB651476
EST:     ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAG                         ACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC
genomic: ACGCACTATTGGATCATCCATTTCTCCCAACATTGTATACTTCATTTCAGgttagactga ... ctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatccagctaatttaaaaaccacaaggttctttactaatgttgtctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTCTTTGCAGTGCTTGATAGGCAACCCATGAAAATTTTCAGGGAAGAATGTG
                                 tactaat  putative branch site (score: 1)
                                            tctattttc  putative PPT
      agctaatttaaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatcagagagtagtttttgtattaacttccatactagtttttcattatccagctaatttaaaaaccacaaggttctttactaatgttgtctattttcagACGCCAACACATGTTTGTCTCATAACAGACTTTTGTCCGGGAGGAGAACTCTTTGCAGTGCTTGATAGGCAACCCATGAAAATTTTCAGGGAAGAATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - -gtttttg
- - - - - - - - - - - - - - tccatac
- - - - - - - - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - - - - - tccagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttgt