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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA

Basic information

species Oryza sativa
transcript LOC_Os06g02380.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G083716_T04 (Zea mays), 3'ss of exon 2
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcatta-gttat-------ttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
||||    | |  |||  | || | | |  |  ||        ||| ||        |||| |||||||||| |||  ||| |       ||||  || |||||||||||| || |||||||| ||||| |||||||||||||| ||||| |||||||||||||| ||||||||||||||||| || || || | |||||| |
gtgaag--cgagcttcgggcactcttttatttgaagacgatgtactgtggcct----ccttcaccaggcactaattgtgttttcgtcttcttctgtatctcagACTGGAGTCAATAAGCTTGCAGACCTAGTTGGAGTTACACTCGGACCGAAGGGAAGGAATGTCGTTTTGGAGAGCAAGTACGGCTCTCCCAAGATTGTTA

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G133698_T02 (Zea mays), 3'ss of exon 2
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagttattt----ctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
|||||||||| |||| ||    |  | |||| | ||   | |     || |  | | |||| ||||||| || |||  || ||     |||||| |||||||||||| || |||||||| ||||| || ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || ||||  ||||| |
gtgagctccacagttttt----atttattatgatataccgatt----tgctgttgacccttaaccaggcgctaattgttttttctcccctacatttcagACTGGAGTCAATAAGCTTGCAGACCTAGTCGGAGTTACACTCGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGTTCTCCTAAAATTGTTA

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgagctccaaagttcttggacacatcttatcaaattttggtcacta---tgattcttagccttgac----caggcactcattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
|| ||   |    || ||  | | |  | ||  ||  ||  |  | |    |   || |   || ||       |   |   || || | | |   |   || |||| || |||||||| || || |||||||| |||||||| ||||| || ||| | ||||||||| | |||||||||||||| || ||  | ||||| |
gtaagtatc---ttttttaaaaaaagttaatggaaacttcattcccaaaccggagctaaaggtttacattttctgtggtttctaattttgtgt-tgtactagGCTGGTGTCAACAAGCTCGCAGATCTTGTTGGTGTTACACTTGGACCCAAAGGACGAAATGTTGTTCTTGAGAGCAAGTATGGATCACCACGAATTGTTA

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
         | | ||  || |   || || |  | |  || | |  ||   | |||   |||        || |||| |  ||| |   | | ||||||| || |||||||| || ||||||||||| || ||||| |||||||| || || ||||||||| | |||||||||||||| ||||| || ||||| |
------gtgagaattaatgaattgattttctggagtaatgattaggattcgttttatttttggttt----ctgattactcgtttgt---tattagACTGGTGTTAACAAGCTCGCGGACCTTGTTGGTGTCACACTTGGACCAAAAGGGAGAAATGTTGTTCTTGAGAGCAAGTATGGATCCCCAAGAATTGTTA

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 2
---------------------gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgacc----aggcact--cattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
                      |  | || | |  |  || ||  || || |  | |  |    | ||   ||  |   | | | |    | |  ||  |||   | | ||     | ||||||||||||||| || |||||||| || || |||||||| || || ||||| || |||||||||||  | |||||||||||||| ||||| |  ||||| |
gtgagtttgtgtgtaaaacacttttgatcaatatgttctgaac--attttgttgattcctatgtattagactttctgatcattatctcttaagtcctaacatctttcaatttcctttttcagACTGGAGTAAATAAACTTGCTGATCTAGTGGGAGTTACTCTTGGTCCAAAAGGCAGGAATGTTGTCCTAGAGAGCAAGTATGGCTCCCCAAAAATTGTTA

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 3'ss of exon 1
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagttatttctac-atgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
||||| |   || |  |   |||  ||   |  | || |  |     ||||   | |   |||        |   |  |  || || | || |||||| || || || ||||||||||| || || || ||||| || || ||||| || |||||||||||| |||||||||||||||||||||| |  ||||| |
gtgagtttgcaactgat--aacatgtcaatttgatttctctttgaagtgatgtattggtgtgatttattggtagcttatgtttccttccatttcagACGGGTGTTAATAAGCTTGCTGATCTAGTGGGGGTTACTCTTGGTCCAAAAGGGAGGAATGTTGTTCTGGAGAGCAAGTATGGGTCCCCGAAAATTGTTA

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 1
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagtta-tttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
            |||    || |    |  ||   | | ||      ||    |  ||| |   |  |   |  |||   | ||| | |    ||| ||||||| |||||||| || || ||||||||||| ||  |||| || || ||||||||||| ||  | |||||||||||||| || || | |||| |||
------------gtttgcagaaaagcttcctc---tctcggat----tggcattgggccattggcgagtttttcttatcgactttttgcgaaacagGCTGGAGTGAACAAGCTCGCGGATCTTGTTGGAGTGACTTTGGGTCCCAAAGGAAGGAATGTCGTCCTCGAGAGCAAGTATGGTTCTCCAAAGATTATCA

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|87009684|gb|CI310787.1|CI310787
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGCGTAAACA-GCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|29632317|gb|CB637326.1|CB637326
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|2312427|gb|C28582.1|C28582
EST:     CCAAGGAGTTGTACTTCACCAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|58596795|gb|CK007323.1|CK007323
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACC
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACC
EST: gi|58612872|gb|CK040584.1|CK040584
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|88336866|gb|CI626946.1|CI626946
EST:     CCAAGGAGTTGTACTTCAACA-GGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAACG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|88404768|gb|CI583575.1|CI583575
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|88694141|gb|CI738179.1|CI738179
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAA
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAA
EST: gi|88574155|gb|CI665924.1|CI665924
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|14571276|gb|BI118644.1|BI118644
EST:     ACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: ACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|88441318|gb|CI602089.1|CI602089
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTAAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|88364381|gb|CI612330.1|CI612330
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCCTGACCTTGCTTGGAGTTACACTGGGACCAA
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGC-TGACCTTG-TTGGAGTTACACTGGGACCAA
EST: gi|66922815|gb|CX109663.1|CX109663
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|58668459|gb|CK057145.1|CK057145
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|58664250|gb|CK052936.1|CK052936
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
EST: gi|58606543|gb|CK034576.1|CK034576
EST:     CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAG                         ACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG
genomic: CCAAGGAGTTGTACTTCAACAAGGATGGCTCGGCTATCAAGAAGCTTCAGgtgagctcca ... tacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcactatgattcttagccttgaccaggcactcattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA
                 ccttgac  putative branch site (score: 4)
                                      ttatttct  putative PPT
                                 attagttatttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctccaaagttcttggacacatcttatcaaattttggtcactatgattcttagccttgaccaggcactcattagttatttctacatgtcagACTGGAGTAAACAAGCTTGCTGACCTTGTTGGAGTTACACTGGGACCAAAGGGAAGGAATGTTGTTTTGGAGAGCAAGTATGGGTCCCCTAGGATTGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG