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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacggggcgttgtttttttctttgaagtggccgtgaggtgaaacattgagagtggttttgtgggtttgttcgagttgtgcggtgaaggaggggaa...

Basic information

species Physcomitrella patens
transcript PP1S363_21V6.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GRMZM2G156333_T01 (Zea mays), 5'ss of exon 4
ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtc------agtacggggcgttgtttttttctttgaagtggccgtgaggtgaaacattgagagtggttttgtgggtttgttcgagttgtgcg-gtgaaggaggggaa
     | |  | || ||    || ||   |   ||||||||||||||||| |||||||||||||||||||| |||||| |||| || ||||| |   |||         ||  | | ||   | |  | ||   |    || ||   |  ||  |    ||    | |    |  ||  | |       ||  ||      |   | 
-----GGAGGCCAAGATCCGCCTCCTCAACGGCACCAACATGGTCGACTATGCCATGGACATCCACAAGTCCCTCTACGACACCGACGACGTGCTCGAGGACATGgtgaagcgccgagccgaggtcgtctccaggctcaggtcgctcgaggaggccgc-agccccgctcgtcgccttcctccagaacccgctcgtcgccccgttca-

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AT3G57290.1 (Arabidopsis thaliana), 5'ss of exon 1
ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacggggcgttgtttttttctttgaa-gtggccgtgaggt-gaaacattgagagtggttttgtgggtttgtt--cgagttgtgcggtgaaggaggggaa
||| |||| || |||||  ||||  ||  | |||| |||||||| || ||||||||||| || ||||||  |||||||||||| || |||| |||||| |||      |      ||| ||  ||| || |  || | ||||  | |     ||| |    | |||||  ||||| |   || |  ||   |    |  |  | 
ATCCTGAAGTCTAAAATCCAGCTTTTGAACCAGACGAACATGGTTGATTACGCCATGGATATTCACAAGAGTCTCTACCACACTGAAGACGCTCCTCAAGgtattcttg------tgtattcctctctggatatgtctgtgaatttgcgtttttgtgtactggtttgtttgtttgatgatgaatgttgaaatttgtggtgatag

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 5'ss of exon 1
ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacggggcgttgtttttttctttgaagtggccgtgaggtgaaacattgagagtggttttgtgggtttgttcgagttgtgcggtgaaggaggggaa
||| | ||  | || || || || ||    |||||||||||||| ||||| ||||||||||||||||||  ||| |||||||| |||||||||||||| |||   |        || |||| | | | | || |    ||   ||     ||| || | |||  | |  |||   |                        
ATCCTCAAGGCCAAGATCGAACTTCTTAATAAGACCAACATGGTTGACTATGCCATGGACATCCACAAGAGTCTTTACCACACCGAGGACGTTCCTCAAGgtacttt-------ttattttatacgtggtagggtttatggcttgtggt-ttgtgatttgtt--gcgatttttggcag----------------------

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ05347 (Selaginella moellendorffii), 5'ss of exon 1
------ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacggggcgttgtttttttctttgaagtggccgtgaggtgaaacattgagagtggttttgtgggtttgttcgagttgtgcggtgaaggaggggaa
      ||  | ||  | || || |||||||||||||||||||||||||||||||||   ||||||||||||      |||||| ||      || || ||  | |||  |    || |    |||    ||    | || || |     |   | |         | | |  |                                
GACCAGATTCTCAAGGCCAAGATCGAGCTGCTGGCCAAGACCAACATGGTCGACTACATGATGGACATCCACCGCAGCCTCTACGAC------GAGGTCCCCAAAGgtaggc---ggcctccatttcgcgctcc--aatgcccatttcccgttccttct-------tctcgcag--------------------------------

upper sequence: PP1S363_21V6.2 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ06230 (Selaginella moellendorffii), 5'ss of exon 1
------ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacggggcgttgtttttttctttgaagtggccgtgaggtgaaacattgagagtggttttgtgggtttgttcgagttgtgcggtgaaggaggggaa
      ||  | ||  | || || |||||||||||||||||||||||||||||||||   ||||||||||||      |||||| ||      || || ||  | |||  |    || |    |||    ||   | |      |   ||      ||      |                                         
GACCAGATTCTCAAGGCCAAGATCGAGCTGCTGGCCAAGACCAACATGGTCGACTACATGATGGACATCCACCGCAGCCTCTACGAC------GAGGTCCCCAAAGgtaggc---ggcctccatttcgcgctccaatgcccatttcccgttcgctcttctcgcag-----------------------------------------

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|100384564|gb|BY987423.1|BY987423
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|18350102|gb|BJ182153.1|BJ182153
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|100375987|gb|BY968260.1|BY968260
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|18358262|gb|BJ190321.1|BJ190321
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|100389405|gb|BY988883.1|BY988883
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|18329284|gb|BJ161290.1|BJ161290
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|19781185|gb|BQ039664.1|BQ039664
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|67568984|gb|BJ941808.1|BJ941808
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|100404357|gb|BY973536.1|BY973536
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|67709902|gb|BJ965718.1|BJ965718
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
EST: gi|67703240|gb|BJ963473.1|BJ963473
EST:     CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGG                         ATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG
genomic: CGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacgg ... agtggtttagATATGGTGGACAGAAGGGCAGAGGTAGTTGGTCGGCTTAAGGTTCTGGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTGAAATCGAAAATTGAGCTGCTGGCCAAGACCAACATGGTCGACTACGCCATGGACATCCACAAGTCTCTCTACCACACAGAGGACGTTCCTCAGGgtcagtacggggcgttgtttttttctttgaagtggccgtgaggtgaaacattgagagtggttttgtgggtttgttcgagttgtgcggtgaaggaggggaa

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA