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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagttgttagtagtcggcttctaattattatcagctaaggcatttccaagagtccagtagtattcacatgtaaatatttgtttctctctgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC

Basic information

species Oryza sativa
transcript LOC_Os02g53060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G374881_T02 (Zea mays), 3'ss of exon 2
tgtagttgttagtagtcggcttctaattattatcagctaaggcatttccaagagtccag---tagtattcacatgtaaatatttgtttctctctgtct--cacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC
   ||    || |  ||  | | |   |  |  |||  | ||||  | ||    | ||    |   ||||||||| |||  | |   | | |   | |  |||||||||||||||||||||| ||||| || ||| |||| ||||| ||||||||||||||
---agaaagtaat--tcctcctttgcatggtgccagagatggcacattcatttttgcaagtttcaaattcacatgcaaaactcttgctattttaatttatcacagGCTGCTGATACACAAGTCATTTCGGACTATATACGTTATTTCCTCCACCAACACAC

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G152775_T04 (Zea mays), 3'ss of exon 2
tgtagttgttagtagtcggcttctaattattatcagctaaggcat-ttccaagagtccagtagt--attcacatgtaaatatttgtttctctctgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC
  |||    || |  ||  | | |   |  |  |||  | | ||  ||||      | |||  |   ||||||||||||  | |   | | |   |  |||||||||||||||||||||| ||||| ||||||||||||||||| ||||||||||||||
-atagaaagtaat--tcctccttttcatggtgccagagatgacacattcctttttgcaagtttttagttcacatgtaaaactcttgctattttaataccacagGCTGCTGATACACAAGTCATTTCGGATTATGTACGCTATTTCCTCCACCAACACAC
















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|88330848|gb|CI636860.1|CI636860
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88421759|gb|CI621403.1|CI621403
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|218499779|gb|FG945547.1|FG945547
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|66924564|gb|CX111412.1|CX111412
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTT
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTT
EST: gi|88721882|gb|CI743394.1|CI743394
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88573296|gb|CI664867.1|CI664867
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|58588610|gb|CF986918.1|CF986918
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88358083|gb|CI605008.1|CI605008
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|58692319|gb|CK081006.1|CK081006
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|25799545|gb|CA755506.1|CA755506
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88309396|gb|CI655764.1|CI655764
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|38477245|gb|CF961378.1|CF961378
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|218498714|gb|FG963991.1|FG963991
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88390264|gb|CI605717.1|CI605717
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|218498950|gb|FG948071.1|FG948071
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|38472737|gb|CF956869.1|CF956869
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88720636|gb|CI743935.1|CI743935
EST:     ACAAGATTACTCACCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTCCCGATTATGTACGCTATTCTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88584075|gb|CI701601.1|CI701601
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAAT
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAAT
EST: gi|33803228|gb|CF327486.1|CF327486
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88302060|gb|CI667906.1|CI667906
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|218504275|gb|FG947024.1|FG947024
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88338208|gb|CI633327.1|CI633327
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|13165514|gb|AU174311.1|AU174311
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88342591|gb|CI655593.1|CI655593
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|88692730|gb|CI736305.1|CI736305
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|218486985|gb|FG965418.1|FG965418
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
EST: gi|14191702|gb|AU183913.1|AU183913
EST:     ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT                         GCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA
genomic: ACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAA

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: 72 (upstream exon), 71 (downstream exon)
Score: 38

GAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCTgtaagtatct ... tgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaagagtccagtagtattcacatgtaaatatttgtttctctctgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC
                                 tttgtttctctctgtc  CT-rich tract
                        atgtaaatatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagttgttagtagtcggcttctaattattatcagctaaggcatttccaagagtccagtagtattcacatgtaaatatttgtttctctctgtctcacagGCTGCTGATACACAAGTAATTTCCGATTATGTACGCTATTTTCTCCACCAACACAC

- - gttgtta
- - - - - - - - cggcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtaa