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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtcatgccaacaagcccctgattcattttttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA

Basic information

species Oryza sativa
transcript LOC_Os03g38020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G098819_T02 (Zea mays), 3'ss of exon 3
---------ttgtcatgccaacaagcccctgattcattttttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
            |  |||| | || ||  |||| ||| |||| |  | | |   ||| || | | |||| |||| ||| |  ||         ||||   |||||||||||||||||||||||||||||||||||| ||||||||||| || ||||| |||||||||||||||||| ||||||| || ||||| |||||||||||||| 
tctgttataaattggtgcccataatcctgtgatgcatatttt-tggaaattagtttatatttagatcatatcatgacagaacaat--------catgaggtttatgcagGTATGAGTACAGATGGGCTGATGGTGTGCAGATAAAGAAACCCATAGAGGTATCAGCACCAAAATATATGGAGTATCTGATGGATTGGATTGAAGGCCAG

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G055125_T02 (Zea mays), 3'ss of exon 4
---ttgtca-----tgccaacaagcccctgattcattttttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
   || | |     |||| | || ||  |||| |||  | |    |       ||| || | | |||  |||| ||| |  ||        |||||   |||||||||||| ||||||||||||||||||||||| ||||||||||| || ||||| |||||||||||||||||||||||||| || ||||| |||||||||||||| 
ctgttataaatcggtgcccataatcctgtgatgcatactcttgggaatccagtttatatttagatcacatcatgacagaacaa--------acatgaggtttatgcagGTACGAGTACAGATGGGCTGATGGTGTGCAGATAAAGAAACCCATAGAGGTATCAGCACCAAAATATGTGGAGTATCTGATGGATTGGATTGAAGGCCAG

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G35130.2 (Glycine max), 3'ss of exon 4
------ttgtcatgccaacaa--gcccctgattcattttttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
       | | |||||||  |     |  ||| |||    |||||  ||| | |||   |||   |  |   | |    |||    |     || | ||  | |  |||||||| || |||||||| ||||||||||| || ||||| || || || || || || ||||||||||| || || |||||||||||||||||||  || 
tgattcctttaatgccaatgacaattctagatccat---ctgtactaaat-atttatgcatt--cctagctcttatgttgtattgtcttttgcacgaaaacttt--agGTATGAATATAGATGGGCAGATGGTGTACAAATTAAGAAACCTATTGAGGTTTCTGCTCCAAAATATGTAGAATATCTAATGGACTGGATTGAAGCACAG

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G34550.1 (Glycine max), 3'ss of exon 4
-----ttgtcatgccaacaag--cccctgattcattttttgtacagaattacttaaatattggtca-tgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
      | | |||||||  ||    |  ||| |||    ||| |  ||| | ||| | ||| ||   | | ||       |  |       ||    | ||||    ||||||| || |||||||| ||||||||||| || ||||| || || || || || || ||||||||||| || ||||||||||||||||||||||  || 
cattcctttaatgccaatgagaattctagatccat---ctgtgctaaat-atttatacattcgtagctcttatgttgtcttgtctttttgcacgaaaacttta----gGTATGAATATAGATGGGCAGATGGTGTACAAATTAAGAAACCTATTGAGGTTTCTGCTCCAAAATATGTAGAATACCTAATGGACTGGATTGAAGCACAG

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G45550.1 (Arabidopsis thaliana), 3'ss of exon 4
--ttgtcatgccaacaagcc-----cctgattcattttttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
   | | |   |||| | ||       ||  | ||||| |||     ||   ||   | || | ||||   |     | ||    |  | |     ||| | |||||||| ||||| |||||||| |||||||||||||| |||||||| || || || || || ||||| ||||| |||||| | ||||| ||||| ||   ||||
aagtatgacttcaactaaccaaaaatatggctgattttctgt-tgctatggattctttctttg-catgctttttgttaatattgtcgaaca-----aatatttgcagGTACGAGTATAGATGGGCAGATGGTGTACAGATCAAGAAGCCCATCGAGGTTTCTGCTCCAAAGTATGTCGAGTACTTGATGGATTGGATCGAGACCCAA

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G19045.1 (Arabidopsis thaliana), 3'ss of exon 4
ttgtcatgccaacaagcccctgattc---attttttgtacagaattacttaaatattgg-tcatgtcataacaaagtaacaacagaaacatggaatttatg------cagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
          ||  || |  || ||     |      ||      |  | || || ||  |||| |  |||| |    |     ||||   |    ||         |||||| || ||||||||||| ||||||||||| || |||||||| || || || ||||| ||||| ||||| || ||| | ||||| ||||| ||    |||
---------aaaagagtctttgtttttgagtgacaattatctcgatgatcaactactgactcatat-gtaactattccattggtgaaatgcgtcggttgcaacgtttcagGTACGAATACAGATGGGCCGATGGTGTACAAATCAAGAAGCCTATTGAGGTTTCAGCTCCAAAGTATGTTGAATACTTGATGGATTGGATCGAGACACAA

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0043g00130.t01 (Vitis vinifera), 3'ss of exon 4
-ttgtcatgccaacaagcccctgattcatttt-ttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
  |||  |     |   ||    |  ||||   |   |  |||   |||  || |||  ||| | |||  || || | ||        |      | | |||||||||||| || ||||||||||||||||| || |||||||| || ||||| || || ||||||||||| || ||| | ||||| ||||||||||  || 
aatgtagttgttgctgaccataaagacattgaatcaaattgaaaaccttctat-ttgtgcat-tgatataaatgtgataattccttattttgtgctttacagGTATGAGTATAGGTGGGCTGATGGTGTACAAATCAAGAAGCCTATTGAAGTTTCTGCTCCAAAATATGTTGAATACTTGATGGATTGGATTGAAGCTCAG

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S213_105V6.1 (Physcomitrella patens), 3'ss of exon 4
ttgtcatgccaacaagcccctgattcattttttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
 |    ||| ||   |     |           |     |||  |     |  | |  |     |    |    |     | ||| ||    |    ||||||||||||  |||||||||| || ||   ||||||||| ||  | ||||| || |||||||| |||||||| || |||||||||||||| ||||| || 
gttctttgcaaatttgaaaacggaaatgggagagacttaaatctcccgcctggtagcgagtgtgtcttgagtgtatggatgcaacgtgattatgggacagGTATGAGTATCGATGGGCTGACGGGGTTACGATAAAGAAACCTTTGGAAGTTTCGGCACCAAAGTATGTGGAATATCTAATGGACTGGATAGAAGGACAG

upper sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 4
----ttgtcatgccaacaagcccctgattcattttttgtacagaattacttaaatattggt-catgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
     | |||   ||  ||      | |  | |||     |     |  ||      | ||   | |  ||  |   |||   ||      | |       ||||||| |||||  ||||||||||||| ||   ||||||||| ||  | ||||| |||||||| || ||||||||||| |||||||||||||| ||||| || 
caaagtttcaaaacagtaatgtagaggtgaagtttcgaatct--cctgtttgggagctagtgtctcttttagtacgataagcgcaacgtttttggg---gcgcagGTACGAGTATCGATGGGCTGATGGGGTCACGATAAAGAAACCTTTGGAAGTTTCAGCACCGAAGTATGTGGAGTATCTAATGGACTGGATCGAAGGACAG

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|27576088|gb|CA998782.1|CA998782
EST:     GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
genomic: GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|218478949|gb|FG952781.1|FG952781
EST:     GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
genomic: GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|218489987|gb|FG956670.1|FG956670
EST:     GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
genomic: GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|1631993|gb|C19722.1|C19722
EST:     GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
genomic: GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|58588740|gb|CF987048.1|CF987048
EST:     GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
genomic: GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|86849659|gb|CI299793.1|CI299793
EST:     GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
genomic: GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|218495086|gb|FG956496.1|FG956496
EST:     CTGAGTTCTGCACACCTGAAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
genomic: CTGAGTTCTGCACACCTG-AGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|25797625|gb|CA753586.1|CA753586
EST:     GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAA                         GTATGAGTACAGATGGGCTGATGGTGTACAGATNAAGAAGCCGATAGAAGT
genomic: GCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGT
EST: gi|8527416|gb|AU092231.1|AU092231
EST:     TGAGTTCTGGCACCCCTGAGAGCTGCCCAAACAATGACTGCTGGCCCAAA                         NTATGAGTACAGATGGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAG
genomic: TGAGTTCT-GCACACCTGAGAGCTGCCC-AACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGAT-GGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAG

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: 70 (upstream exon), 72 (downstream exon)
Score: 63

CTGTGGATTTCTTTAACCAAGTTAACCTGCTGTACGGCACACTCGCTGAGTTCTGCACACCTGAGAGCTGCCCAACAATGACTGCTGGCCCAAAgtacgttatt ... atttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA
                        aagtaac  putative branch site (score: 63)
                                            aatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtcatgccaacaagcccctgattcattttttgtacagaattacttaaatattggtcatgtcataacaaagtaacaacagaaacatggaatttatgcagGTATGAGTACAGATGGGCTGATGGTGTACAGATAAAGAAGCCGATAGAAGTATCAGCACCAAAATATGTGGAGTACCTAATGGACTGGATTGAAGGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - catgcca
- - - - - - caagccc
- - - - - - - - - - tgattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgga