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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA

Basic information

species Oryza sativa
transcript LOC_Os06g05180.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 6
gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtc-atggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
  |   ||||| ||   |  | |  || |   || | |       ||| ||||||  || ||||||| | |  ||||  ||  |||||||||||||||| ||||| ||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||| |||||||||||||
-gtacatttttgtactgaggtgtatgt-tctgaattttttgttgctctatgcagtattatgatggtgcgttttatggcaaagtagGTCTGGGATTACCAGACGAAAAGCTGTGTTCAGACACTTGAAGGGCATACACATAACATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 7
gttttttttttctatccacttttgagtgttccaagtatcc-acgattctgtgcagtcctaagatggtgtggtc-atggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
    |    || | | | |   ||  ||||   ||| |   |   |||| | |||||||||| ||||||| |  ||||  ||  |||||||||||||||| ||||||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||| |||||||||||||
---gtacaattttgtactcagctgtatgttttgagtgtttgattgttctatccagtcctaaggtggtgtgctttatggcaaaatagGTCTGGGATTACCAGACGAAGAGCTGTGTTCAGACACTTGAAGGGCATACACATAATATTTCTGCTGTTTGTTTCCATCCTGAGCTCCCTATAATCATTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G419984_T01 (Zea mays), 3'ss of exon 6
gttttttttttctatccacttttgagtgttccaagtatcc-acgattctgtgcagtcctaagatggtgtggtc-atggtgaaccagGTCTGGGATTA---------CCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA-------------------------------------------------
    |    || | | |    |||  ||||   ||| |   |  ||||| | |||||||||| ||||||| |  ||||  ||  |||||||||||||         ||| |||||||| |||||||||||||||||||| |||||||| || ||||||| ||||||||||||||||||||| |||||||||||||                                                 
---gtacaattttgtacttagttgtatgtttggagtgtttgattattctatccagtcctaaggtggtgtgctttatggcaaaataggtctgggattaatccgattaccagacgaagagatgtgttcagacacttgaagggcatacacataatatttctgttgtttgtttccatcctgagCTCCCTATAATCATTACTGGATCTGAAGATGGTACAGTTCGTATATGGCATTCGACAACTTACAG

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 7
----------------------gttttttttttctatccacttttgagtgttc-caagtatccacgattctgtgcagtcctaagatggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
                      | | | | |   | | | | |||   | | |  |  |||  |    | ||   ||   ||| ||||  ||    |  |||| ||||| |||||||| || || || || ||||| ||||| || ||||| || ||||||||  | |||||||| || || |||||||| ||||||||||||||||
gttttgttttcatttgttgcttgatctatctgcttgtacgcatttacatatacatacatatatatatatatgaaaaggaataacatgg-atgaaacttatgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 7
--------------gttttttttttctatccactt-ttgagtgttc-caagtatccacgattctgtgcagtcctaagatggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
                ||  ||  ||||||  ||| | | |    | ||   |  |||   | ||   ||   ||| ||||  ||    |   ||| ||||| |||||||| || || || || ||||| ||||| || ||||| || ||||||||  | |||||||| || || |||||||| ||||||||||||||||
gttttgttttcatttgttgcttaatctatctgcttgtcgcgcacacgcacacacacacatgtatgaaaaggaataacatgg-atgaaacttacgaatcagGTATGGGATTATCAGACCAAAAGTTGTGTCCAGACCCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTTCCTATAATCATTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 7
----------------gttttttttttctatcca-cttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatgg------tgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
                 | ||||||| || | || |||     |  |     |  | |    | | |   |     |  |  | ||   ||        |||| ||||| ||||| || ||||| || || ||||| ||||| || ||||| || ||||||||  | ||||||||||| || |||||||| || |||||||||||||
gtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTTTGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 7
---------------gttttttttttctatcca-cttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatgg------tgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
                 | |||||| || | || |||     |  |     |  | |   || | |   |     |  |  | ||   ||        |||| ||||| |||||||| ||||| || || ||||| ||||| || ||||| || ||||||||  | |||||||| || || |||||||| || |||||||||||||
gtttgttttctattttctgttttttcctcttcatcttccctctaatttggtttcctatatttgtatatggataggaattattatgccgataaaacctttgaatcagGTATGGGATTATCAAACCAAAAGTTGTGTCCAGACTCTAGAAGGTCACACACACAATGTATCTGCTGTATGCTTTCATCCTGAACTACCTATAATCATTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 7
----gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatggtgaac---cagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
    | || |  ||    | |   | |  ||| |   | |  ||       | || | |    |||| || |  |  ||||       ||||| ||||| || ||||| || || ||||| ||||| || || || || ||||||||  ||||||| || ||||||||||| |||||||| ||||| || |
gtatgcttctggttaagcttccaatatctgtgctttgattcccctgagaattatgta-tttgcagatcgtttactagtggtactttttcagGTATGGGACTATCAAACCAAAAGTTGTGTCCAGACGCTAGATGGGCACACACACAATGTTTCTGCCGTATGTTTCCATCCAGAGCTTCCAATAATAATCA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------------------------------gttttttttt-tctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgt---ggtcatggt---------gaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
                                               || |  || | | ||||  | |||  || ||    ||||  | | |  ||    ||  |  | | || |   | ||||            ||| ||||| |||||||||||||| ||||| || |||||||| || ||||| |||||||||||  ||||||| || | ||| ||||| ||||| |||||||| ||||
gtctgtactgagctttcttgcttctttgcaagttgtttgctacatatgtgtgcttgtatgtatctccattt--gtattgtttgtatataggttcgtgcagggttttctgtttgtatattgttcataaatttcttctggaagcagGTGTGGGATTACCAAACAAAGAGTTGCGTTCAGACTCTCGAAGGTCATACACACAATGTTTCTGCAGTATCTTTTCATCCAGAGCTACCTATAATTATTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 7
---gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtg------tggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
       |  | ||| ||   |||||   || | ||  | | |  ||   | ||   |   | | |  |       ||    | ||||| ||||||||||| |||||||| || || ||||| ||||| || || || || ||||||||  | ||||| || ||||||||||| |||||||| || || || |
gtatgcctcctgttcaatggtcttttagttgatacatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcagGTCTGGGACTACCAAACAAAAAGTTGTGTACAGACCCTGGAGGGGCACACACACAATGTATCTGCAGTATGTTTCCATCCAGAGCTTCCAATTATAATCA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 7
gttttttttttctatccacttttgag-tgttccaagtatcca--cgattctgtgcagtcctaag---atggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
|| |    ||  ||   | |||  || |||    |||||  |  || ||   |  |     | |   ||||     || |    |  ||||| ||||| || ||||| || || ||||| |||||||| ||||| || ||||||||  ||||||| || || ||||||||||| ||||| ||||| || |
gtctgccgttgataattattttcaagctgtgtttagtatttatgcggtttgatagaaggaaatgttcatggacaaatcctccaaatgcagGTGTGGGACTATCAAACCAAAAGTTGTGTCCAGACACTGGAAGGCCACACACACAATGTTTCTGCAGTCTGCTTCCATCCTGAACTTCCCATAATAATAA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 7
gttttttttttctatccactt-ttgagtg--ttccaagtatccacgattctgtgcagt--cctaagatggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
|| ||| | |  |    | |   | | |   |||||  |||   | ||||  |    |  | |    || |    |  ||||| | ||||| ||||| |||||||| || || |||||||||||||| ||||| || ||||||||  ||||| | || ||||||||||| ||||||||||| ||  |||
gtgtttatctgatgcttattgactaaatagcttccatttatgtgc-attccatttgattactttctgtgattaaattttggtggaacagGTGTGGGACTACCAAACCAAAAGTTGTGTTCAGACACTAGAAGGCCACACACACAATGTTTCTTCAGTCTGTTTCCATCCAGAGCTTCCTATTATTTTTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S61_1V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------------------gttttttttttctatccacttttgagtgt--tccaagt--------atccacgattctgtgcagtcc--taag--atggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
                                                                                                |  |||||  |    ||    | | |||  |||| ||        ||  |   |  |||| ||| |  |||   |   | |  || | ||    ||||| |||||||| || || |||||||| ||||| ||||| ||||||||||| |||||| | ||||| ||    ||||||||||| || || || ||| |||
gtaatgactttatcttgtctgttgctaatcttaattctccaggtcaatataactgaaagacttggttctataaggctttcgggatttgcatgagtatcatttttgacatagcatgacttactgtaatccatgttcgattaaatgtattctgatgtgtagttcagtaacttacaattttttccttgtcgggcagGTTTGGGATTATCAGACCAAGAGCTGCGTTCAAACACTGGAAGGACATACTCACAACGTATCTGCAGTGGCATTCCATCCTGACCTGCCAATTATCCTTA

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------gttttttttttctatccacttttgagtgttccaagtatccacg-att--ctgtgcagtcctaagatggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA
             ||  | |||   |    |    |  ||  | |||||     |  |||   ||   |||           | | ||    |||  ||||| |||||||||||||| ||||||||||| |||||  | || || ||| | || ||  | ||||| || ||||||||||||||||| || || ||  | |
cgacgtggtaaacgtcatgtttaagtgaagatcacttggtcattcaagttgttgcatattgattgcttagtttcccttcctggcgttctctttgatgcagGTGTGGGATTACCAAACCAAGAGCTGTGTGCAGACTTTAGAGGGTCATTCTCATAATGTGTCTGCAGTGTGTTTCCATCCTGAGCTCCCCATCATTTTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttttttctatccacttttgagtgttccaagtatccacgattctgtgcagtcctaagatggtgtggtcatggtgaaccagGTCTGGGATTACCAAACGAAGAGCTGTGTTCAGACACTTGAAGGACATACACACAACATTTCTGCTGTTTGTTTCCATCCTGAGCTTCCTATAATCATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT