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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagggttttggacctcatttctgaggtagattagggcttgattgtggtaatctttggaatgtgaatttgtaattggttctgtctcgtgttctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTGATGCGGAGCTGAAGTTGGTCGGAGAGTACGGTCTCCGCAACAAGCGTGA

Basic information

species Physcomitrella patens
transcript PP1S223_95V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S223_95V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ11758 (Selaginella moellendorffii), 3'ss of exon 1
cagggttttggacctcatttctgaggtagattagggcttgattgtggtaatctttggaatgtgaatttgtaattggttctgtctcgtgttctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTGATGCGGAGCTGAAGTTGGTCGGAGAGTACGGTCTCCGCAACAAGCGTGA
                                   |   |  | |  |  ||  | | || ||     ||     | ||  ||  |||| |       |||||| |||||||| |||||||| ||  |||| |||||||| ||||| || || |||||||| ||| |||| || ||||| || || ||||||||||| ||
-----------------------------------gtaagtctctccttctcgatcgcat-tgcgcccgtgcc--gatcgatccggtgtgcc----gcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA

upper sequence: PP1S223_95V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ13465 (Selaginella moellendorffii), 3'ss of exon 1
cagggttttggacctcatttctgaggtagattagggcttgattgtggtaatctttggaatgtgaatttgtaattggttctgtctcgtgttctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTGATGCGGAGCTGAAGTTGGTCGGAGAGTACGGTCTCCGCAACAAGCGTGA
                                   |   |  | |  |  ||  | | || ||     ||     | ||  ||  |||| |       |||||| |||||||| |||||||| ||  |||| |||||||| ||||| || || |||||||| ||| |||| || ||||| || || ||||||||||| ||
-----------------------------------gtaagtctctccttctcgatcgcat-tgcgcccgtgcc--gatccatccggtgtgcc----gcagATGGGAAAACTTTCAAGAAGCCACGGCGGCCATTCGAGAAGGAGCGCCTGGACGCGGAGCTCAAGCTGGTGGGCGAGTATGGCCTGCGCAACAAGCGCGA
















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|18364215|gb|BJ196288.1|BJ196288
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|18349649|gb|BJ181699.1|BJ181699
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|162264964|gb|FC441467.1|FC441467
EST:     TTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: TTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|67724298|gb|BJ974557.1|BJ974557
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|162272878|gb|FC448021.1|FC448021
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|67712588|gb|BJ966037.1|BJ966037
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|18373816|gb|BJ205394.1|BJ205394
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|162226468|gb|FC402435.1|FC402435
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|67695897|gb|BJ956130.1|BJ956130
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|208379745|gb|DC907630.1|DC907630
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|37844303|gb|BJ602311.1|BJ602311
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|162226467|gb|FC402434.1|FC402434
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|162264963|gb|FC441466.1|FC441466
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCTTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|37828611|gb|BJ586623.1|BJ586623
EST:     ATGGTGCACGTCGCTTCNTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: ATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|18344000|gb|BJ176039.1|BJ176039
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|67572524|gb|BJ945348.1|BJ945348
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|208349758|gb|DC921522.1|DC921522
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|162259505|gb|FC435016.1|FC435016
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|18351681|gb|BJ183733.1|BJ183733
EST:     CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: CTCCGTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
EST: gi|162260365|gb|FC435017.1|FC435017
EST:     TCCGCTTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATT                         ATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG
genomic: TCCG-TTAGTTTCAACACCAAAATGGTGCACGTCGCTTCCTTCCGCAATTgtaagcctcg ... ctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaatctttggaatgtgaatttgtaattggttctgtctcgtgttctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTGATGCGGAGCTGAAGTTGGTCGGAGAGTACGGTCTCCGCAACAAGCGTGA
                                    tctcgtgttcttttt  CT-rich tract
                  aatttgtaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagggttttggacctcatttctgaggtagattagggcttgattgtggtaatctttggaatgtgaatttgtaattggttctgtctcgtgttctttttatagATGGAAAAACTTTTAAGAAGCCCCGTAGGCCCTTCGAGAAAGAGCGTCTTGATGCGGAGCTGAAGTTGGTCGGAGAGTACGGTCTCCGCAACAAGCGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG