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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaactatatgattgctgaagcactgattgttatatgtcattttaaaggattgttttgttggatattgattttggaatggcattgtattttcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g38960.1
intron # 1
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 1
lower sequence: GRMZM2G013600_T01 (Zea mays), 3'ss of exon 1
acaactatatgattgctgaagcactgattgttatatgtcattttaaaggattgttttgttggat-attgattttggaatggcattgta--ttttcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
       | ||||  || ||      ||| |||| | |    |  |||  |    | |||| || ||||  |||   ||   | |||   ||||  | | ||| |||||||||||||| ||||||||||||||||||
-ggttcttctgatcactcaaatgtctatttttatgtatacact--aagtttcacatggttgtatcattggatttatgatcttactgttccttttgttatacagCTATGAGGATGAGCCTCCAGAACCTGAGATTGAG

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G086904_T01 (Zea mays), 3'ss of exon 1
acaactatatgattgctgaagcactgattgttatatgtcattttaaaggattgttttgttggat-attgattttggaatggcattgtattttcc--tctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
       | ||||  || ||       || |||  | |    |  |||  |    | |||| || ||||  |||  |||   |||||  |||    | | |||||||||||||||||| |||||||| |||||||||
-ggttcttctgatcactcaaatgtcactttttacttatacact--aagtttcacatggttgtatcattggatttacaatcttattgttctttttgttatacagGTATGAGGATGAGCCCCCAGAACCGGAGATTGAG

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G38350.2 (Glycine max), 3'ss of exon 1
acaactatatgattgctgaagcactgattgttatatgtcattttaaaggattgttttgttggat--attgattttggaatggcattgtattttcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
|  | |   | ||   | ||   ||     |     ||   ||        ||| |  ||  ||  | || |||   | ||| ||      |     |||||||| ||||||||||||||||| || |||||||||
atcagt-cgtcatgcttcaattgctagggttagagcgttgattctgtaatctgtatgttttcattgaatggtttctca-tggaataaagggtggtggtgcagGTACGAGGATGAGCCACCAGAGCCCGAGATTGAG

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G51940.1 (Arabidopsis thaliana), 3'ss of exon 1
-acaactatatgattgctgaagcactgattgttatatgtcattttaaaggattgttttgttggatattgattttggaatggcattgtatttt--cctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
   |||  ||   |   |||   |  |  | || | |   | | ||   | || | | ||  || | |  |     ||| | |    ||||   |   ||||| ||||||||||||||| |||| ||||||||||| 
agaaaccctaatttcattgagaaaaag-ctattttttaaaactctatgagcttttctagt--gaaacttgtgagtaaattgaagaaaatttgggctattgcagATATGAGGATGAGCCAGCAGAGCCTGAGATTGAA

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv16s0100g00530.t01 (Vitis vinifera), 3'ss of exon 3
acaactatat-gattgctgaa-gcactgattgttatatgtcattttaaaggattgttttgttggatattg--attttggaatggcattgtattttcctc-tgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
      || | |||| | ||| | ||    ||  || |   ||    |    |  | || | | ||| ||  |||||  |       || |||||  |  ||||| |||||||||||||| ||||| ||||||||||| 
----tcatgtagattacagaatgtaccatatga-atgtacaatggctatctgtaatattatagcatagtggaattttaaatatttgatgaattttgttgatgcagATATGAGGATGAGCCGCCAGAGCCTGAGATTGAA

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:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|88727042|gb|CI750697.1|CI750697
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|88762358|gb|CI771914.1|CI771914
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218497334|gb|FG955294.1|FG955294
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218499405|gb|FG963729.1|FG963729
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|163923301|gb|EG709356.1|EG709356
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|163927473|gb|EG713889.1|EG713889
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|163918386|gb|EG715314.1|EG715314
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|58681466|gb|CK070153.1|CK070153
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|38481397|gb|CF965486.1|CF965486
EST:     CAACGACAT-GACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: CAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218496317|gb|FG954187.1|FG954187
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATTGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|25798016|gb|CA753977.1|CA753977
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACCACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218487224|gb|FG954426.1|FG954426
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218491289|gb|FG948708.1|FG948708
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|86904845|gb|CI310638.1|CI310638
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|58600678|gb|CK011206.1|CK011206
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218490022|gb|FG965705.1|FG965705
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|88456045|gb|CI567761.1|CI567761
EST:     GAGGCGGGGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|163928871|gb|EG711933.1|EG711933
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218498533|gb|FG957594.1|FG957594
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|88325209|gb|CI646631.1|CI646631
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|163917777|gb|EG711299.1|EG711299
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|88296235|gb|CI667625.1|CI667625
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|218484046|gb|FG946740.1|FG946740
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|33805453|gb|CF328603.1|CF328603
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|88302670|gb|CI668516.1|CI668516
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|58686251|gb|CK074938.1|CK074938
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|163920983|gb|EG710396.1|EG710396
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|163918487|gb|EG710289.1|EG710289
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
EST: gi|58602936|gb|CK013464.1|CK013464
EST:     GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGG                         GTATGAGGATGAGCCACCAGAACCTGAGATTGAG
genomic: GAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG

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: 73 (upstream exon), 68 (downstream exon)
Score: 76

CGCTTGGCCGCCGTGCGGCGAAACCCTAGCGATTGTAGCGGCCGGAATCAGAGGCGGCGGAAGCCATGGCGGACGACGACTACAACGACATGGACATGGGgtttgcctta ... tcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggattgttttgttggatattgattttggaatggcattgtattttcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG
                  tattgat  putative branch site (score: 76)
                                     ttgtattttcctct  putative PPT
                 atattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaactatatgattgctgaagcactgattgttatatgtcattttaaaggattgttttgttggatattgattttggaatggcattgtattttcctctgcagGTATGAGGATGAGCCACCAGAACCTGAGATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - -tgctgaa
- - - - - - - - - - - -ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggcatt