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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC

Basic information

species Oryza sativa
transcript LOC_Os01g32800.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 2
tagctgaatgtttcaatcttggattacttcaa--caac-catatgcttagggtttta-actgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
      | | |  |||| ||  |||  | |||  ||   ||  ||||     || |  |||  |  |   |  |   |||||||   ||    |||| | |||||| || ||||| ||||| ||||||||||||||||||||| |||| || ||||| ||||| ||||| ||||| |||||||| || ||||| || ||||| |
---taaagtttgccaattttatattgttccaagtcatttcacctgctgctatttctgtactcttttgtc-ttttatgattctaatatcaccttttcttctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATCACTGATTTTGAGACCAAGATTAATCTGCTCAAGCTTGCCCATTTTGCGGTGATAGCTTCTC

upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G868757_T07 (Zea mays), 3'ss of exon 1
---tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcc---cacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
   | ||  ||| ||  ||| ||  ||  | ||      ||  ||||  |  ||||      |      |  |   ||||||| | ||   ||| | |    |||||| || ||||| ||||| ||||||||||||||||||||    ||||| ||||| ||||| ||||| |||||||||||||| || ||||| ||  |||| |
agcttgccaaat-ttataattttccatgtcatc-----tcacctgctgcgatttttgcaatcttttgtcttttatgattctaatgccacctatttttcatctacagACCGGAGACACTATCATTCAGCTCTACAACAATTTCATTGTCGACTTTGAGACCAAGATTAATCTGCTCAAACTTGCCCATTTTGCGGTGATAACTTCTC

upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G34310.2 (Glycine max), 3'ss of exon 2
tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAA---ACTTGCCCACTTCGCGGTCATCGCTTCAC
       ||| || |||     ||||  ||| |||    || |  ||  ||| |   ||    ||| | |   |  ||  |  ||||  | ||   | ||  |  || ||  ||  |  |     | ||     |  |   |  ||| |||  |    |||      ||||   ||| |    |  |||    |       | 
----gtgatgctttaatac--aattatatca-caatttcat-cacagactttgagacgaaaatcaaccttctcaagcttgca-cattt-tgctgttatagTTTCTCGGCAGTATTCTGAAAA---AGAAGCTGCTGTTGGTTATCTTGGAGGGGTCATTCAGAAACTTCAAGACACTAGAGAGCAGCGCATAGAAGAACCTAT

upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G34310.1 (Glycine max), 3'ss of exon 1
--tagctg--aatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattct---cccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
  |  ||   | ||   |||| ||    ||||   |    ||||| ||||   || ||  | |     | |  |   |  | |||||   |   | |       ||| |||| ||  |  | |||||  | ||  ||||||||||| | ||||| |||||||| ||||| |||||||| ||||| || || || || || | ||| |
gttgacttctattgaaacaatattca--tactctgatgtgcatattctta---ttatagtttaaatttatttgtttga--caaacggttcttcctataaattttcagGCTGGTGATGCTTTAATACAATTATATCACAATTTCATCACAGACTTTGAGACGAAAATCAACCTTCTCAAGCTTGCACATTTTGCTGTTATAGTTTCTC

upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G45620.2 (Arabidopsis thaliana), 3'ss of exon 1
---------tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
           | |  ||   ||||| ||| ||| ||||  |||   | ||  |  | | |||||   ||  || |  |  |||   |      ||||||      ||| |||| ||  |  | || ||| ||||  ||||||||||| ||||||| |||||||||||||||||||| || ||||| || || || ||  | |  || |
ttaggttttagggtttatagatcaattttg-attgcttc--caagtttttgtgtctgatcttaacctgtgt-cattgttataatataattttttttcattt-----cagGCTGGTGATGCTTTGATTCAGTTCTATCACAATTTCATCACTGACTTTGAGACGAAGATCAATCTTCTGAAGCTTGCGCATTTTGCTGTGGTGGTCTCTC

upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G19006.1 (Arabidopsis thaliana), 3'ss of exon 1
tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggc-aatcctgcaattctaacggcattcattc-----tcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
     |||| ||| |     |   |||   || |  ||  |    | |||||  || |||  |  |||   |   |||   | |  |   |||          ||| |||| ||  |  | |||||||| ||||||||||||||| ||||||| ||||||| |||||||||||| || ||||| || ||||| ||  | |  || |
----cgaatattttagctcagagatacccaaaaactcagctttacaaggttt--acagatttgttaatgacgtgtttccccctgtttatgttcataatctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAGACGAGGATCAATCTTCTGAAGCTTGCGCATTTCGCTGTTGTAGTCTCCC

upper sequence: LOC_Os01g32800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 3'ss of exon 1
tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcatt-cattctc--ccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
    ||  |||| |     |||||    | ||   | ||||   |       || |   |      |  |  ||  || |     ||  ||| ||     ||| | || ||  |  |||| ||| | ||  | ||||| ||| ||||||| ||||| ||||||||||||||||| || || || || || ||||| | |||  
---ttgcttgttcctgatgtggatgttatgaaattcaatatctgtgcatgcatatcctttttatggttatctaaaacttattcttttgtattttcatttgcagGCGGGTGATGCTCTCATTCAGTTATATCATAATTTTATCACTGACTTTGAGACTAAGATCAATCTTCTCAAGCTCGCACATTTTGCTGTCATAGTTTCTA

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|86906557|gb|CI291086.1|CI291086
EST:     ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAG                         ACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgcactt ... tctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
EST: gi|88353023|gb|CI630201.1|CI630201
EST:     ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGNCCAG                         ACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgcactt ... tctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
EST: gi|88332118|gb|CI643535.1|CI643535
EST:     ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGNCCAG                         ACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgcactt ... tctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
EST: gi|88572393|gb|CI663964.1|CI663964
EST:     ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAG                         ACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgcactt ... tctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
EST: gi|88359854|gb|CI617765.1|CI617765
EST:     ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAG                         ACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgcactt ... tctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
EST: gi|88434204|gb|CI589269.1|CI589269
EST:     ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAG                         ACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgcactt ... tctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG
EST: gi|88434226|gb|CI589291.1|CI589291
EST:     ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAG                         ACTGGCGACACCATCATACAGCTCTA-AACAATTTCATCTCTGACTTCGAG
genomic: ACCAGCTCACCCTCAAGCTCGACCACTTCCTCCAACTCCCCGCCGCCCAGgtctgcactt ... tctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC
                             ttctaac  putative branch site (score: 1)
                                        ttcattctccc  putative PPT
                           aattctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagctgaatgtttcaatcttggattacttcaacaaccatatgcttagggttttaactgatgggcaatcctgcaattctaacggcattcattctcccacagACTGGCGACACCATCATACAGCTCTACAACAATTTCATCTCTGACTTCGAGACGAAGATCAATCTTCTCAAACTTGCCCACTTCGCGGTCATCGCTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA