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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaggagatggtttgcaattgcaatatgttatatacatatgtcctacacatgcattttcaaaacatcgaattaatggtcaactattttgtttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os08g41950.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41950.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G159397_T01 (Zea mays), 3'ss of exon 2
---tgaaggagatggtttgcaattgcaatatgttatatacata-tgtcctacacatgcattttcaaaacatcgaattaatggtcaactattttgtttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG
   ||| |   |   |    |    || | || | |  | ||| | |  |  ||| |   || |     ||     |||   |  |  ||    ||| ||||||||| |||||  |||||||||||| |||||||||||||||||| | ||||| |||||||| |||||||||||
ttatgaggcctaatatagagatcatcattgtgatctcaatatagtttgttgaacaaggcattcctgtttat---gctaaacatacataatgacattt-tttcagCAACTGAAAAGTAGCCGCAATGAGTACCTCAAACTGAAGGCACGTGTTGATAATTTACAGCGGACTCAAAG
















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|88592982|gb|CI711128.1|CI711128
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88401388|gb|CI585944.1|CI585944
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88722826|gb|CI746336.1|CI746336
EST:     AATGCAGTTACGCAGGACCCGAAACAGGTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGGAATGAATACCTCAAACTGAAGGCA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCA
EST: gi|58663584|gb|CK052270.1|CK052270
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88720377|gb|CI743676.1|CI743676
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88694062|gb|CI738100.1|CI738100
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAAT
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAAT
EST: gi|88721563|gb|CI744862.1|CI744862
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAA
EST: gi|88696368|gb|CI739943.1|CI739943
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAA
EST: gi|88984144|gb|CI723700.1|CI723700
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGG
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGG
EST: gi|88694250|gb|CI738288.1|CI738288
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATG
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATG
EST: gi|88722944|gb|CI746454.1|CI746454
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACT
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACT
EST: gi|88725198|gb|CI748457.1|CI748457
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGA
EST: gi|40491399|gb|BX901494.1|BX901494
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88719988|gb|CI745287.1|CI745287
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAAT
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAAT
EST: gi|88671413|gb|CI725529.1|CI725529
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88694823|gb|CI738861.1|CI738861
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCG
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCG
EST: gi|163926627|gb|EG713643.1|EG713643
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88687916|gb|CI731492.1|CI731492
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88724225|gb|CI747484.1|CI747484
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAAC
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAAC
EST: gi|24208827|gb|AU225854.1|AU225854
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88722014|gb|CI745417.1|CI745417
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTACCCGCAATG
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATG
EST: gi|88461647|gb|CI695489.1|CI695489
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88730563|gb|CI754176.1|CI754176
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAA
EST: gi|88726869|gb|CI750524.1|CI750524
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88718586|gb|CI742096.1|CI742096
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCA
EST: gi|88904617|gb|CI711916.1|CI711916
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCA
EST: gi|88718424|gb|CI741934.1|CI741934
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGG
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGG
EST: gi|88581317|gb|CI698295.1|CI698295
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88720603|gb|CI743902.1|CI743902
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCC-GCAATGAATACCTCAAACTGAAGGCAAGGGTTGA
EST: gi|66932169|gb|CX119017.1|CX119017
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88313445|gb|CI671563.1|CI671563
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88728398|gb|CI751908.1|CI751908
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88338971|gb|CI677788.1|CI677788
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
EST: gi|88581413|gb|CI698397.1|CI698397
EST:     AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAG                         CAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA
genomic: AATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 71 (downstream exon)
Score: 145

CATGACTAAAACGCTTGAGAAGTATCAGAAATGCAGTTACGCAGGACCCGAAACAGCTGTCCAAAATAGAGAAAGTGAGgtaattatta ... tttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacacatgcattttcaaaacatcgaattaatggtcaactattttgtttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG
                        aattaat  putative branch site (score: 145)
                                     ctattttgtttctttc  putative PPT
                                      tattttgtttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaggagatggtttgcaattgcaatatgttatatacatatgtcctacacatgcattttcaaaacatcgaattaatggtcaactattttgtttctttcagCAATTGAAAGCTAGCCGCAATGAATACCTCAAACTGAAGGCAAGGGTTGAAAATTTACAACGGACTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - -gtttgca
- - - - - - - - - - - - - - - - - - catatgt
- - - - - - - - - - - - - - - - - - - - - -cctacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacatc