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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttactgacttttatacaccagtatgcattttttcccatgtgatcaacatgaagaacgaactgacatcaatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGCAAACATAGAAGCTCAACTGAAGAAGATTGAG

Basic information

species Oryza sativa
transcript LOC_Os04g45070.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G116538_T02 (Zea mays), 3'ss of exon 3
-gtatgttact--gacttttatacaccagtatgcattttt-----tcccatgtgatcaacatgaa----------gaacgaactgacatcaatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGCAAACATAGAAGCTCAACTGAAGAAGATTGAG
  | | ||| |  || | |||    ||| ||    ||  |         || |     |  || |          |||  ||  | ||  | | |  ||||||| | |||||  |||||| ||||||||| ||||||||||||||||||||||||||||||||| || ||||||||||||||
gatgtcttatttagattcttaatatccaatagaagttgatataatctatatataggtgatgtggattcctaacttgaattaatgggcacaattatgacagGGCTACTAAGAAAGTATCTGTTATTCTTTCATGGGAGAACACAAAGAAAGCAAACATAGAAGCTGAAATGAAGAAGATTGAG

upper sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G122937_T01 (Zea mays), 3'ss of exon 3
-----------gtatgttactgacttttatacaccagtatgcattttttccc----atgtgatcaacatgaa---gaacgaactgacatcaatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGCAAACATAGAAGCTCAACTGAAGAAGATTGAG
           |  | | | |  |   || |      |||  |   |   |     |||||   |     ||   |||  ||    ||| | |||  ||||||| | |||||  |||| ||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||||||||||
tatcatatttagattctcaatatccaatagaagttgatataaaccataggcaggagatgtggaaattcctaacttgaattaatacgcataactgtgacagGGCTGCTAAGAAAGTATCCGCTATTCTTTCATGGGAAAACACAAAGAAAGCAAACATAGAAGCTGAACTGAAGAAGATTGAG

upper sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G122937_T02 (Zea mays), 3'ss of exon 3
-----------gtatgttactgacttttatacaccagtatgcattttttccc----atgtgatcaacatgaa---gaacgaactgacatcaatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGCAAACATAGAAGCTCAACTGAAGAAGATTGAG------------------
           |  | | | |  |   || |      |||  |   |   |     |||||   |     ||   |||  ||    ||| | |||  ||||||| | |||||  |||| ||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||||||||||                  
tatcatatttagattctcaatatccaatagaagttgatataaaccataggcaggagatgtggaaattcctaacttgaattaatacgcataactgtgacagGGCTGCTAAGAAAGTATCCGCTATTCTTTCATGGGAAAACACAAAGAAAGCAAACATAGAAGCTGAACTGAAGAAGATTGAGGTATGTCATTGAAGGAAT

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|86528410|gb|CI168616.1|CI168616
EST:     AGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: AGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|38471757|gb|CF955888.1|CF955888
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|58585685|gb|CF983993.1|CF983993
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|88975844|gb|CI024095.1|CI024095
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|50878545|gb|AF527706.1|AF527706
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|88968318|gb|CI098560.1|CI098560
EST:     TGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|87010775|gb|CI312467.1|CI312467
EST:     TCATTGATCANAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|87026567|gb|CI252521.1|CI252521
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|58693172|gb|CK081859.1|CK081859
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|29684469|gb|CB680744.1|CB680744
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|89167373|gb|CI252904.1|CI252904
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|29670320|gb|CB666595.1|CB666595
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|38470437|gb|CF954568.1|CF954568
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|58603482|gb|CK014010.1|CK014010
EST:     TCATTGATCAAAGCATGGGAGGAAAATGA-AAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|38471661|gb|CF955792.1|CF955792
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|88445327|gb|CI587221.1|CI587221
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGA-AAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|86478310|gb|CI120943.1|CI120943
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|86528486|gb|CI168692.1|CI168692
EST:     GAGAAGACAAAAGCTGAGCACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: GAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|89189973|gb|CI013540.1|CI013540
EST:     GGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: GGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|86256047|gb|CI007763.1|CI007763
EST:     ATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCGGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: ATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|29670321|gb|CB666596.1|CB666596
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACCCAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|313084059|gb|HO213842.1|HO213842
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|89165064|gb|CI255121.1|CI255121
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|58696071|gb|CK084758.1|CK084758
EST:     TCAAAGCATGGGAGGAAAATGAGAAGACCAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|88216477|gb|CI216326.1|CI216326
EST:     AAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: AAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|88992545|gb|CI035633.1|CI035633
EST:     TGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACCAAGAAAGC
genomic: TGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|38470061|gb|CF954192.1|CF954192
EST:     CAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: CAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|88367239|gb|CI564003.1|CI564003
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|58601478|gb|CK012006.1|CK012006
EST:     TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|88839566|gb|CI005354.1|CI005354
EST:     GAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: GAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
EST: gi|163923100|gb|EG712799.1|EG712799
EST:     TCATTGATCAGAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA                         GGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC
genomic: TCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGC

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), 57 (downstream exon)
Score: 276

ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAAgtatgttact ... aatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGCAAACATAGAAGCTCAACTGAAGAAGATTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcattttttcccatgtgatcaacatgaagaacgaactgacatcaatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGCAAACATAGAAGCTCAACTGAAGAAGATTGAG
                                   aactgac  putative branch site (score: 276)
     tttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttactgacttttatacaccagtatgcattttttcccatgtgatcaacatgaagaacgaactgacatcaatgtcgcagGGCTTCGAAGAAGCTATCTGCTATTCTTTCCTGGGAGAACACAAAGAAAGCAAACATAGAAGCTCAACTGAAGAAGATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG