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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtcgttgtgccttgtggtgtatagaagctggccgtgtgcgaagggttttgggtcttaaacaagctcttgatgatcatttatcagatacttttactgatttgctgtggtgttccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACGATCAGCGACTTGCCTGCAGGAATACGGCAGGCTGTTGAATTG

Basic information

species Physcomitrella patens
transcript PP1S4_62V6.1
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|162161404|gb|FC337610.1|FC337610
EST:     AACAAGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAG                         ATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
genomic: AACAAGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAGgtgcgtcgtt ... ccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
EST: gi|162191494|gb|FC367185.1|FC367185
EST:     AGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAG                         ATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
genomic: AGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAGgtgcgtcgtt ... ccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
EST: gi|162197210|gb|FC372523.1|FC372523
EST:     CGTCTAGCAGTTCCTGAG                         ATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
genomic: CGTCTAGCAGTTCCTGAGgtgcgtcgtt ... ccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
EST: gi|162192881|gb|FC369875.1|FC369875
EST:     AACAAGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAG                         ATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
genomic: AACAAGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAGgtgcgtcgtt ... ccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
EST: gi|100382413|gb|BY969102.1|BY969102
EST:     ATTACGGTGACAACAAGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAG                         ATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG
genomic: ATGACGGTGACAACAAGGGATTGTTCGGAAGGCGTCTAGCAGTTCCTGAGgtgcgtcgtt ... ccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgatcatttatcagatacttttactgatttgctgtggtgttccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACGATCAGCGACTTGCCTGCAGGAATACGGCAGGCTGTTGAATTG
                         tactgat  putative branch site (score: 2)
                                         tgttcctt  putative PPT
      atcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtcgttgtgccttgtggtgtatagaagctggccgtgtgcgaagggttttgggtcttaaacaagctcttgatgatcatttatcagatacttttactgatttgctgtggtgttccttgagcagATGTTTGATCGGAAGTATGTTGAAGCTATCCTACAAGAGTGGTTCCGGACGATCAGCGACTTGCCTGCAGGAATACGGCAGGCTGTTGAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT