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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC

Basic information

species Physcomitrella patens
transcript PP1S79_253V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g19840.1 (Oryza sativa), 3'ss of exon 1
--------tgcagcaatagtttctagtgtggcagctgtggccccagggact----ggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggt-tttgtag-
         |   |     |||| |  |   ||   |  | | |   || |    | | ||  | ||| ||    | |  ||   ||   |  ||| |  || || |||| ||    | ||  ||||||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     | |    
gtaaccgacgattcctccatttccatcgcctcattcgatgtctctttgatttatcgatcttcgttttcttcccctgattcctgatttttttcgtttgttcgtcgtctttgaagGATTCGGGGGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGGATCAAGAAGCCCAAGCGCCACCGCCAGA----

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G009894_T01 (Zea mays), 3'ss of exon 1
-------tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgat-tgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC
       | | ||| |    || | | ||       | |       |   |   |    ||   ||   |     |||  | ||| |    |||   | |    |   | |   ||||||| ||||| ||||||||||| |||||||||||||| ||||||   |||||||| || |||||||||   |||   ||     |      
gtaactctccggcactccgctcga-tctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG-----

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G147791_T01 (Zea mays), 3'ss of exon 1
------------tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC
              |  |  | | |   |   |    | ||||      |        ||       || ||     |    |||||  |   ||| |  |  |   |   | ||   | ||||| ||||| ||||||||||| |||||||||||||| | ||||   |||||||| || || |||||    |||   ||     |      
gtaattctcaggcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgc-actttgttggcagGCATCCGGAAG---AAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G147791_T02 (Zea mays), 3'ss of exon 1
tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC
                           ||||      |        ||       || ||     |    |||||  |   ||| |  |  |   |   | ||   | ||||| ||||| ||||||||||| |||||||||||||| | ||||   |||||||| || || |||||    |||   ||     |      
--------------------------gtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgc-actttgttggcagGCATCCGGAAG---AAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G147791_T03 (Zea mays), 3'ss of exon 1
-tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC
   |  |  | | |   |   |    | ||||      |        ||       || ||     |    |||||  |   ||| |  |  |   |   | ||   | ||||| ||||| ||||||||||| |||||||||||||| | ||||   |||||||| || || |||||    |||   ||     |      
gcaccccgctcgatctcatcctaatcggtgtgattttcgtcttcaccgtcaacccacccctccacttactctgattcgc-actttgttggcagGCATCCGGAAG---AAATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTTCAAGGCGCACAAGAACGGCATTAAGAAACCCAAGCGCCACCGCCAG-----

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G068496_T02 (Zea mays), 3'ss of exon 1
tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattga----ctgatttttctgtggttttgtagCAGGTA----AGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC
        ||  | || || |  |  | | | || |     | ||  | | ||||| |||   | | | ||| | ||    | | |   |  | |   | |    ||| |     |||||| ||||| ||||||||||| ||||| |||||||| | ||||   |||||||| || ||||||||                        
-------gta-ctcctcgtcttcctcccgagtcctcct---ccggattcgatgttcgtctcctgatttattggtggaaccgcagGTGACTAGGAGCAGTAGCGAGAGGGATTCTGGATGGCCAAGTCGAAGAACCACACGGCGCATAACCAGTCGTTCAAGGCGCACAAGAACGGCATCAAGAA------------------------

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G37060.1 (Glycine max), 3'ss of exon 1
tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC------
                 ||  |     |       |    ||    ||| ||  |  | ||  | | |||| |||| || |  ||       ||   | ||||   ||||||| ||||| ||||||||||| || ||||||||||||||||||  |||||||||||| ||||| |||   |||| |||     |||  ||      
-----------------gttcgctctgttcaatttctctaac--acgttcttacttttttgctgctctcttcattgtcttacattgtgtgcattgaattgcag-

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA17G03550.2 (Glycine max), 3'ss of exon 1
tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC------
                     |   ||| ||  |  |    ||    ||||| |  || ||| | | || |  |    |  |     | ||    |  |   |   ||||||| ||||| ||||||||||| || ||||||||||||||||||  ||| |||||||| ||||| |||   |||| ||||    |||  ||      
---------------------gttcgctctgtgcaaattctctaac-ttgttctcactttgttgatttcctcttcatttcgtaacattttgtgcattgaattgcagAGATGGCAAAGTCGAAGAACCACACCGCTCACAACCAGTCCTACAAGGCCCATAAGAATGGCATCAAAAAGCCAAAGAGGCATCGCCACACTTCCACCAA

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G15320.1 (Glycine max), 3'ss of exon 1
tgcagcaatagtttctagtgtggcagctgtggccccagggactg-gtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC------
        ||  ||| | |   | | |     |  |      || |  ||||| |     |  |  | || |  |    | ||||| || |  |||| | ||||   ||||||| ||||| ||||| ||||| |||||||| ||||||||||||  |||||| || || ||||||||    |||| ||||    |||  ||      
---gttcgtatcttcaatttctgtaacaaattcttctaattttgcgctttgttctattctttcccttctcatcgtcctttcattttgctcta-ttttattgcag-

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA09G04280.1 (Glycine max), 3'ss of exon 1
---tgcagcaatagtttctagtgtggcagctgtggccccagggactg-gtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC------
    |   |   | |||||   ||| ||       |  |      || |  || ||  |  |||     |  | |  |    | |||||| ||    ||  | ||||   ||||||| ||||| ||||| ||||| || ||||| ||||||||||||  |||||| || || ||||||||    |||| ||||    |||  ||      
gttcgtttcttcaatttct---gtgacaaaaaattcttctaattttgtgctttttttctgttcttctcttcccatcgtcttttaatttttgtgccacttgattgcag-

upper sequence: PP1S79_253V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv07s0005g01340.t01 (Vitis vinifera), 3'ss of exon 1
tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC----
                 ||   ||  |||   |    || |     |  |  |||  | ||      |||   |  | |  |     |    |  |||||      | ||||||||||| |||||||||||||| |||||||||||||||||   |||||||||||| ||||||||       |||||     ||| |||    
-----------------gtacagcctctgcatcttttggtaa-aacgacgccgtt--tttgctcccatctcactgaattcttccactttcaatgctgtagGG----AAATGGCGAAGTCGAAGAACCACACTGCCCACAACCAGTCCTACAAAGCCCACAAGAATGGAATCAAGAAACCCCGAAAGCACCGCCACACCTCCACC

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|67573153|gb|BJ945977.1|BJ945977
EST:     ATATTGTTTGAGTCGCCTCGTCTGCGTCTTAG                         CAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
genomic: ATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... ggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
EST: gi|67691427|gb|BJ951660.1|BJ951660
EST:     TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTT--                         -AGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
genomic: TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... ggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
EST: gi|67696537|gb|BJ956770.1|BJ956770
EST:     TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTTAG                         CAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
genomic: TTTCTGCGTCGCACTGTAATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... ggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
EST: gi|67508207|gb|BJ941078.1|BJ941078
EST:     ATATTGGTTTGAGTCGCCTCGTCTGCGTCTT--                         -AGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
genomic: ATATT-GTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... ggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
EST: gi|67693178|gb|BJ953411.1|BJ953411
EST:     GAGTCGCNTCGTCTGCGTCTT--                         -AGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
genomic: GAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... ggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
EST: gi|7584238|gb|AW700135.1|AW700135
EST:     ATTGTTTGAGTCGCCTCGTCTGCGTCTT--                         -AGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
genomic: ATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... ggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
EST: gi|162268442|gb|FC444315.1|FC444315
EST:     ATATTGTTTGAGTCGCCTCGTCTGCGTCTT--                         -AGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA
genomic: ATATTGTTTGAGTCGCCTCGTCTGCGTCTTAGgtgcgttgtt ... ggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC
                              gactgat  putative branch site (score: 3)
                                 tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcagcaatagtttctagtgtggcagctgtggccccagggactggtgttgttgttcctctgtcggtgtcttgattgactgatttttctgtggttttgtagCAGGTAAGATGGCGAAGTCCAAGAACCACACTGCGCACAACCAGTCCTACAAGAACCACAAGAATGGTATCAAGAAGGTTAAGAAGCATAAATACATCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
tgcagca