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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcgtggttgagcttaaggcctttcgaaatccctccgcccggcccttttattttgtttttcagaatctcaggatgggactgatacgcattggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCAGTTCTGCTGTCGCTGTTTCTGCTATTCAAGTTCTTACCGAAAGATCTGA

Basic information

species Physcomitrella patens
transcript PP1S47_5V6.1
intron # 2
splice site 3'
intron type U2

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|18357303|gb|BJ189362.1|BJ189362
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|18357467|gb|BJ189526.1|BJ189526
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|18344957|gb|BJ176998.1|BJ176998
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|100431216|gb|BY960085.1|BY960085
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|18356652|gb|BJ188711.1|BJ188711
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|100388316|gb|BY951918.1|BY951918
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|100423679|gb|BY976504.1|BY976504
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|208389036|gb|DC937369.1|DC937369
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|162248338|gb|FC422553.1|FC422553
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|67572635|gb|BJ945459.1|BJ945459
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|18343415|gb|BJ175453.1|BJ175453
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|162211220|gb|FC386932.1|FC386932
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|100368970|gb|BY984964.1|BY984964
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|18358244|gb|BJ190303.1|BJ190303
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|162242981|gb|FC417621.1|FC417621
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|18375136|gb|BJ206714.1|BJ206714
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
EST: gi|18368931|gb|BJ201016.1|BJ201016
EST:     TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCG                         GAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA
genomic: TGACGGTGTTCATAGGATGTCATCGGTCTGTGAAGCCCGCTCCTCCCTCGgtaagttttc ... ggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattttgtttttcagaatctcaggatgggactgatacgcattggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCAGTTCTGCTGTCGCTGTTTCTGCTATTCAAGTTCTTACCGAAAGATCTGA
                               gactgat  putative branch site (score: 3)
     ttttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcgtggttgagcttaaggcctttcgaaatccctccgcccggcccttttattttgtttttcagaatctcaggatgggactgatacgcattggtggtgcagGAGACGATGTCGAAAGAGCATGCGATGCGATTCCCTTTCATCGGCAGTGCAGTTCTGCTGTCGCTGTTTCTGCTATTCAAGTTCTTACCGAAAGATCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT