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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcagaggccaatgttttgctgccctggacttaatcagtgagtgtataagttagtgtcattgccgggaaattgaagttgacttgagaataatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAGTTGTGGAGACTGTAGAGCTGAACGAGCATGCGATAATTTGGAGTCTTAG

Basic information

species Physcomitrella patens
transcript PP1S140_59V6.2
intron # 1
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|18375328|gb|BJ206906.1|BJ206906
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
EST: gi|18360935|gb|BJ192999.1|BJ192999
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
EST: gi|18363548|gb|BJ195620.1|BJ195620
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
EST: gi|18372892|gb|BJ204494.1|BJ204494
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
EST: gi|18360763|gb|BJ192826.1|BJ192826
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
EST: gi|18327203|gb|BJ159205.1|BJ159205
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAG
EST: gi|18365718|gb|BJ197795.1|BJ197795
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
EST: gi|18374115|gb|BJ205693.1|BJ205693
EST:     AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAG                         GGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG
genomic: AAGGTTTTTGGTGTGGATCTGAGAAGTCGGAGGTGGAATTTGGATCCCAGgtgaggtgca ... taatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtataagttagtgtcattgccgggaaattgaagttgacttgagaataatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAGTTGTGGAGACTGTAGAGCTGAACGAGCATGCGATAATTTGGAGTCTTAG
                               agttgac  putative branch site (score: 4)
                                                tcttc  putative PPT
                                           aataatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgcagaggccaatgttttgctgccctggacttaatcagtgagtgtataagttagtgtcattgccgggaaattgaagttgacttgagaataatcttcagGGGATACCGTAACGAAGAGCGCGTAGGATTTGGCCATTATCATAGCAGGAGTTGTGGAGACTGTAGAGCTGAACGAGCATGCGATAATTTGGAGTCTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - -tgctgcc