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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacacattgctatcctcatgcagtgatgttatctgttaatggaaaagaactgatggagttctgttcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTTGTAGGGGCAGAGGCTGAAGATAAGGAACAAGAAAAAACTCAGCGCCCAC

Basic information

species Oryza sativa
transcript LOC_Os03g38960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G086904_T01 (Zea mays), 3'ss of exon 2
------------------------gtacacacattgctatcctcatgcagtgatgttatctgtta-atgg--aaaagaactgatggagttctgttcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTTGTAGGGGCAGAGGCTGAAGATAAGGAACAAGAAAAAACTCAGCGCCCAC
                         |||    ||| | |     ||||  |   |  |  | ||| ||||  || | |||  ||| |  |||||| ||    ||||||| |||||||| || |||||||| ||||| |||| ||||||||| ||  |||| |  |||| ||||||||||||||| ||||| ||  ||||   ||
gtgcaggcacattactattgttttatacttttatt-caacttctatgctttataggaagatattatatggccaatacaaccaatgtacctctgttgaa---cagGAAGGAGCTGAAGAAGAGCCTGAGAACAACGAAGATGCCCCTGATGACGTCATAGGTGGTGAGGGTGAAGATAAGGAACAGGAAAAGACCAAGCGTGAAC

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G013600_T01 (Zea mays), 3'ss of exon 2
--gtacacacattgctatcctcatgcagtgatgttatctgttaatg------gaaaagaactgatggagt---tctgttcaat------------aatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTTGTAGGGGCAGAGGCTGAAGATAAGGAACAAGAAAAAACTCAGCGCCCAC
  | | ||||||| ||||  |  |  | |  | ||     || |||         ||||  | ||        |    |||||            || |||||||||| ||||| || | |||||| ||||| |||| ||||||||| ||  |||| | ||||| ||||||||||||||| ||||| ||  ||||    |
gtgcagacacattactattgttttatacttttattcaacttttatgcttcataggaagagtttatatgaccaatacaatcaatgtacttctgttgaacagGAAGGGGCCGAAGAAGAGCTTGAGAACAACGAAGATGCCCCTGATGATGTCATAGGTGGAGAGGGTGAAGATAAGGAACAGGAAAAGACCAAGCGTGAGC
















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|218495985|gb|FG958579.1|FG958579
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|88727042|gb|CI750697.1|CI750697
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|88762358|gb|CI771914.1|CI771914
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|218497334|gb|FG955294.1|FG955294
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|218499405|gb|FG963729.1|FG963729
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|163923301|gb|EG709356.1|EG709356
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|163927473|gb|EG713889.1|EG713889
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|163918386|gb|EG715314.1|EG715314
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|58681466|gb|CK070153.1|CK070153
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAAGAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAAT---AACGAGGATGGCCCTGATGAG
EST: gi|38481397|gb|CF965486.1|CF965486
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAAGCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|218496317|gb|FG954187.1|FG954187
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGA-AATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|25798016|gb|CA753977.1|CA753977
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|218487224|gb|FG954426.1|FG954426
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|218491289|gb|FG948708.1|FG948708
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|86904845|gb|CI310638.1|CI310638
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|58600678|gb|CK011206.1|CK011206
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|218490022|gb|FG965705.1|FG965705
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|88456045|gb|CI567761.1|CI567761
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|163928871|gb|EG711933.1|EG711933
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|218498533|gb|FG957594.1|FG957594
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|88325209|gb|CI646631.1|CI646631
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|163917777|gb|EG711299.1|EG711299
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|88296235|gb|CI667625.1|CI667625
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|218484046|gb|FG946740.1|FG946740
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|33805453|gb|CF328603.1|CF328603
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|88302670|gb|CI668516.1|CI668516
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|58686251|gb|CK074938.1|CK074938
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG
EST: gi|163920983|gb|EG710396.1|EG710396
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|163918487|gb|EG710289.1|EG710289
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTT
EST: gi|58602936|gb|CK013464.1|CK013464
EST:     GTATGAGGATGAGCCACCAGAACCTGAGATTGAG                         GAAGGGGCTGAAGAGGAACCTGAGAATAACAATGAGGATGGCCCTGATGAG
genomic: GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAAC---GAGGATGGCCCTGATGAG

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: 68 (upstream exon), 52 (downstream exon)
Score: 55

GTATGAGGATGAGCCACCAGAACCTGAGATTGAGgtacacacat ... tcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTTGTAGGGGCAGAGGCTGAAGATAAGGAACAAGAAAAAACTCAGCGCCCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagtgatgttatctgttaatggaaaagaactgatggagttctgttcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTTGTAGGGGCAGAGGCTGAAGATAAGGAACAAGAAAAAACTCAGCGCCCAC
                            aactgat  putative branch site (score: 55)
                                       ttctgttc  putative PPT
                                            ttcaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacacattgctatcctcatgcagtgatgttatctgttaatggaaaagaactgatggagttctgttcaataatagGAAGGGGCTGAAGAGGAACCTGAGAATAACGAGGATGGCCCTGATGAGGTTGTAGGGGCAGAGGCTGAAGATAAGGAACAAGAAAAAACTCAGCGCCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA