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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA

Basic information

species Oryza sativa
transcript LOC_Os06g01480.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G440219_T01 (Zea mays), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
   | || ||   |  | |   || | |    |||| | |    |  | | |||  || |   |  |   ||  | | |  |       | ||| |  |     |||||    ||| |  |    || ||  | |  | ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||  |||||||   
acaaatattcgagaacggagacac-tactgctatat-acattctttcagagtatg-gtatatcacatcctcctacgacacatgcacattattattatta-----gcagACAAGTGCAGACTG---GGAGGCCCTGGTGAGGAGGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACCCGGACCAACCG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
           ||  || | | | ||     | ||| ||   | | |  | || |  | | ||  ||  |  |  ||| |     |  || | |     |   |         |    ||   |||   | | ||   || || |||||| ||||||||||||||| || || || ||||||||||| || ||||| ||  | |||||            
-----------gtttagcaggaaaat-----cctatcatc--tctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataat-ttagAGTTATGCAAGATAGGAAACGAAG-AGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S1_447V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------------------------------gtcagtac-tcagtacagtacgtaca-tgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagc-cagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
                                                                                  |||||   | |  |  | ||  |   ||  | |      | |   || |      |    ||   | || |  ||   | || ||||   || | |   |||     ||||    ||| ||||    | ||   |  |    ||| | || ||||| |||||||||||||||||||| ||||| ||||||||  |||| |   |  | ||   
gtaagaatcgatcagaatcctcggtgtactatgtatgacaccagactagaaaacacgtcctcacatgcttcgttgccccatttcagtctattaagattgaactcatggtgtgttcgagccctgggattgcaattagattccatgtccactacgtacacggacaagtaaccccga-tgtggtcat-----cagAAGTGTGCAGGATTGGGGACGACCCACC---AGAGAATCAAAACGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCCTCGGGCAATCGAGCGAACCG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S102_187V6.1 (Physcomitrella patens), 3'ss of exon 1
----gtcagtactcagt-acagtacgtacatgcatg-catatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCG--------GAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA-------------
    |    | |||| |   || || ||  ||  |  |  ||          || | | || || |    |||  |     |    || |    ||  |||  ||    |     ||| || | |    |||  || |||| | ||        || || ||||  || ||||||||||||||||||||||| ||||| || ||    ||||   |  | ||             
gcatgaacatgctcatttgaaggacatatttgagtttcgaatttctcccacatagagtttttgttttgggattg-gtggatatc--ttgatactgatgatattca-atttttgtggcgatgtcaggggtatgcagGATCGGGGACGTCACCACCGAAGACCAGAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAATATCCTTGCGGGAACCGTGCAAATCGAGCCACCGCC

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S6_458V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------gtcagtactcagtacagtacg-----tacatgcatgcatatg-atagatgtgtaca-atattcgtgtgctaattaagccagcaataatta-actgggagta-taaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
                                                             | ||||  |  ||| ||     || ||  ||  ||||| ||| || | || | ||||   | ||  |||      || | | || | ||     ||| |  |   |    |||||   ||| | ||    | ||     ||  | ||| | |||| ||| ||||||||||||||||||||||||||||| || || || || |   |  | ||   
gtaagccaacgaacccacattttgcaggatttcattaacgttggttgaggttagaaaactggaactcgctttagttcgaggaatatataaatagatatggatatatatatatatatatatatatgagaatactctaagtactgataacaccatctgtacttgcggcgacatcagAGGTGTGCAGAATTGGCGACGA---CGCACCCGAGAATCAGAGCGACTGGTACTTCTTCAGCCACAAGGACAAGAAATATCCTACTGGAAACCGCGCAAACCG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S223_12V6.2 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------gtcagta--ctcagtac--agtacgtacatgcatgcatatgatagatgtgtacaatattcg-tgtgctaattaagccagcaata-attaact-------gggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
                                                    |||| ||   |  | ||   | || ||     | | |   ||| ||     |||  |   | |||| || || |  |   | |  || | ||       ||| ||  || ||||||  |||| | ||||   ||| | | ||  ||       ||| |||| | ||| |  ||||| ||||| | |||||||||||||||||||||||| |   |  ||||   
gtatgcaacaattcatttcagagtattcgtagcatttttcatgttgagggatgtcaatagatttgggacccggaacatagccttaagaactggattgaaaaccacaccacctgatgtgatatttgactccatacttcatcacctaaaattcgggtgttaaatcatgca-acagATCTTTGCAAAATCCAGGCCGACTCAAA---TGAGAAGCAAACCGATTACTACTTTTTCAGTCGCAAGGACAAGAAGTACCCGACGGGCAACCGCGCCAACCG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S182_37V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------gtcagtactcagtacagtac-gtacatgca--tgcatatgatagatgtgtacaatattcgtgtgctaattaa--gccagcaataattaa-ctgggagtataaccatgcatgcagAGCGTTG-CCGGATCAATGGCGGGTCGGCGGCG--------GAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
                                                                    | |  | | |  |||||||  | |||  |  ||      | | | |   |  |   |  | | || ||  |  |  ||||  || |   |  | |||||   ||   |      ||   |  | ||    ||  || |||| | ||        ||| | || |  || ||||||||||||||||||||||| |||||||| || || || |   |  ||||   
gtaagcatcggaatcctgaaggtagtatggtgcagtgttcaacctcctcatctagtttcgtcaaaaaataaacatttaaaacagtactatccattgaattgtgatcaacataagctcaagagcatgttctcctcatctattgatagcatgaaatggtccagcagtattgacaaaaacttgttgcaccgatcagAAGTGTGCAGGATCGGGGACGACGCACCAGAGCATCAAAGTGACTGGTACTTCTTCAGCCACAAGGATAAGAAGTATCCCACAGGAAACCGTGCCAACCG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaag----ccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---
          ||  ||  ||   || |     |  |||   | ||| |      | ||   | ||  |||       |  ||   ||||||  ||  |  ||||   |||||||   |||  |||    ||||      | | | |    |||||| | ||||||||||| ||||| ||||||||||||||||| || || |   |  ||||   
-------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgt--ccat---tgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAAC---CAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ32131 (Selaginella moellendorffii), 3'ss of exon 1
----gtcagtactcagtacag-tacgtacat-gcatgcatatgatagatgtgtacaa-tattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
    | | ||  ||  |  || | |  |  | | |   | |  |  | | | |  || | || | || |||| |    |  |  | | |  |   ||    ||    |  |||    |     | || |  || ||  | |||  ||  ||||||| |||| |||||||||||||||||||| |||||||| |||||||| ||||||||||||||            
gtaagacggtcatccctcaagcttctcatttcggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatg--aattgcgtttgccacaca----cagAACGGTGCCGAATTGGCTCCGC-GGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
                                             |||   || ||   | |   |  |         |    ||||  |       |||   |        ||| | ||  | ||   | ||||   | |  || || | |||||||||||| ||||| ||||||||||||||||| || ||||| ||  | |||||            
---------------------------------------------gtagtctagtctcctccatttcgatatgattgcacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGG-ATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ37712 (Selaginella moellendorffii), 3'ss of exon 1
--------gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaa-tattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
        ||||   ||||   |    | |    | |   | |  |  | | | |  || | || | || |||| |    |  |  | | |  |   ||    ||    |  |||    |     | || |  || ||  | |||  ||  ||||||| |||| |||||||||||||||||||| |||||||| |||||||| ||||||||||||||            
gtaagacggtcatccctcaa-gcttctcatttcgggaaaaaaaaaaccgttctttggaagtctttgcgttctaaatgtctcttctctcactgccatcgatg--aattgcgtttgccacaca----cagAACGGTGCCGAATTGGCTCCGC-GGAGCAGCACGAGTGGTACTTCTTCAGCCACAAAGACAAGAAATACCCGACCGGGACGAGGACCAACAGAGCCACCGG

upper sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA------------
                                             |||   || ||   | |   |  |       | |    ||||  |       |||   |        ||| | ||  | ||   | ||||   | |  || || | |||||||||||| ||||| ||||||||||||||||| || ||||| ||  | |||||            
---------------------------------------------gtagtctagtctcctccatttcgacatgattacacaccactgacacctctttcattgttcttcgattttggcagAGAAGTGTAAGATCGG-ATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA
                      aataattaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaagccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT