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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaaaactagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC

Basic information

species Physcomitrella patens
transcript PP1S317_21V6.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os11g03734.1 (Oryza sativa), 3'ss of exon 10
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaag-aggaatgtaagctgagaaaactagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC
          |   ||  ||||     | ||     || | ||  | | | |  || |    |     ||  || || ||    ||   | |    ||||| |||||||| ||||||||||||||||||||||||||||||||||| || || || || ||| | |||  || ||||    |||| |  ||  |     | 
----------gttagtattcatggtt-tagtactttactt-tgtttaggattctagcatctgttctctctttgacaattaatgtgtaaatctaaaaaccagCTGGAACCCAGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os12g03480.1 (Oryza sativa), 3'ss of exon 13
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaaa-actagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC
    |   ||  |  |  || ||| | |  |         | | |||  |    |   |  |     ||||  |   |||     |   |||| | ||||| |||||||| ||||| ||||||||||||||||||||||||||||| || || || || ||| | ||   || ||||    |||| | ||| ||     | 
----gttagtatacatggtcttatactttctt---tgttcaaggattctagc--atctgtttcctctctgactattgctaatgtataaatgtgataaccagCTGGAACCCAGATGCGATTGTCTTCAACTCCTGGCAACAGTATGGAACTCCTAGTTATTGGATGCAGACATATTTCCGTGAATCAAGCGGTGCTATGATT

upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 15
tacagaaggtgaaggtcatca--tatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaa-aactagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC
        || |    | |    | | |||  |  |     ||  | |     ||   |  | ||     ||||    |||||||  |   |||| ||| ||| |||||||| ||||||||||| ||||| ||||||||||||||||| || || || || ||| | |||  || ||||    |||| |  ||  |     | 
--------gttagtacctttggctttgccttttttattttctaacattcttcttgttcacaagtgc---ttgagtttgactagctc-tgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: LOC_Os12g03530.1 (Oryza sativa), 3'ss of exon 13
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaa--atgaagaggaatgtaagctgagaaaactagctgg---tctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC
              || |  |  |||  | | |  |   | |   |  ||   |   |  |     |||      |   |  || |   |   |||  ||| ||| |||||||| ||||||||||| ||||| |||||||| |||||||| || || || || ||||| ||   || ||||    |||| |  ||  |     | 
--------------gttagtacctccagctttgctcctttttatttccaacgttcttgttggtcacaagtacgcgagtttgactagaccttaatgtaatgatcagCTGGAACCCAGATGCAATTGTGTTCAATTCCTGGCAGCAGTATGGCACTCCTAGTTATTGGGTGCAGACATATTTCCGTGAATCAAGTGGTTCTGTGATT

upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 14
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaaaac--tagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC
       | |     || |  | |   |        || | |   ||    |   |  |     | |||| ||  |   |   | |        | || ||| |||||||| || || ||||||||||||||||||||||| ||||| || || ||||||||| | ||     |||||    | || | |||||||    | 
-------gttagtattcttggttttttttaccctctacttgttcttt----tcccgttgctctaacgctgcgatgattttgtttcgaacaaaacgagatcagGTGGAACCCGGACGCTATTGTCTTCAACTCCTGGCAACACTATGGAACTCCTAGCTACTGGATGCAGACGATTTTCCGCGAGTCAAGCGGCGCCATGATT

upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 15
tacagaaggtgaaggtcatcatatccctcgtggaac---acgtatgaattgaaatgaagaggaatgtaagctgagaaaactagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC
                     |||| |||    |      |||  |||| |  |   ||  |||  ||||   | ||    |  | ||     ||||   ||| |||||||| |||||||| |||||||||||||  || |  ||||| ||||| ||||| ||||||||||  |||||     | || | ||| ||    || 
--------------------gtatctctcacttacttttccgttcgaatggttactcag--gaagataaggcaataatctcaaattgttaaattggtt-tcagGTGGAACCCTGATGCAATAGTCTTCAACTCCTCTCATCTATATGGAACACCTAGCTATTGGGTTCAACGGTTTTTTGCAGAGTCAAGCGGAGCAACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaatgaagaggaatgtaagctgagaaaactagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC
              aatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagaaggtgaaggtcatcatatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaaaactagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA