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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtcaaattttaggatctgcatgtgaaatcttacctatcctagacctgaatgacgtcagtttttcaatttttagaagtacaatatatgattgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG

Basic information

species Physcomitrella patens
transcript PP1S22_326V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EDP05070 (Chlamydomonas reinhardtii), 3'ss of exon 2
----ggtcaaattttaggatctgcatgtgaaatcttacctatcctagacctg-aatgacgtcagtttttcaatttttagaagtacaatatatgattgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG
    ||      |   |    || |   |  | |   ||      ||   || ||||||   | |||  | | || | ||    |  |  ||| || |   ||||| ||| |  | || ||| | || || || || ||||| |||||||||||||| |||||||||||||||
gctcggaggcgctcacgctcatggactggcgaccaggccagctgcagctgtgtaatgac--tattttaccgagttgttgat---cgttggatgcttcttgcgcagGCAAGCGCCGCTACGACCGCAAGCAGTCGGGTTACGGTGGTCAGACCAAGCCCGTCTTCCACAAGAAG
















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|18368682|gb|BJ200767.1|BJ200767
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|162262338|gb|FC437665.1|FC437665
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|162228552|gb|FC404150.1|FC404150
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|18335674|gb|BJ167694.1|BJ167694
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|18360736|gb|BJ192799.1|BJ192799
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|162225415|gb|FC401193.1|FC401193
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|162221524|gb|FC397541.1|FC397541
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|67575316|gb|BJ948140.1|BJ948140
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|67698779|gb|BJ959012.1|BJ959012
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
EST: gi|18327408|gb|BJ159410.1|BJ159410
EST:     CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAG                         GTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC
genomic: CCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTTTGTACGCACAAGgttttgttct ... tgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaatgacgtcagtttttcaatttttagaagtacaatatatgattgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG
              tttttcaatttttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcaaattttaggatctgcatgtgaaatcttacctatcctagacctgaatgacgtcagtttttcaatttttagaagtacaatatatgattgtatggcagGTAAGAGGAGATATGACAGGAAACAATCAGGATACGGAGGTCAGACCAAGCCTGTCTTCCACAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG