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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtacacggtccagaattgcacctctttgatttcgactttctctttcgtttgccgacaactgtcttgaagaatggctttctgtcgcgttagctctgccgtgctctagtttcacatctctgtggttttgggaagcagtgaagttacggattatttctaataattgagattctttgttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCAGGAGGTTTGGACCTTGAAGACGAAGTGGGGCAAAAACGTGAAGGCAGTC

Basic information

species Physcomitrella patens
transcript PP1S6_398V6.2
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|162208390|gb|FC384702.1|FC384702
EST:     ATGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAG                         GGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
genomic: TTGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAGgcaagtacac ... gttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
EST: gi|162155505|gb|FC331495.1|FC331495
EST:     ATGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAG                         GGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
genomic: TTGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAGgcaagtacac ... gttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
EST: gi|162178312|gb|FC354718.1|FC354718
EST:     CAATCTCTCAATCTCGGACAG                         GGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
genomic: CAATCTCTCAATCTCGGACAGgcaagtacac ... gttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
EST: gi|162160190|gb|FC337087.1|FC337087
EST:     ATGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAG                         GGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
genomic: TTGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAGgcaagtacac ... gttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
EST: gi|100370808|gb|BY948526.1|BY948526
EST:     TTGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAG                         GGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA
genomic: TTGCCCAAGTTTACCGCCTCTTTATTCAGCAATCTCTCAATCTCGGACAGgcaagtacac ... gttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaagcagtgaagttacggattatttctaataattgagattctttgttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCAGGAGGTTTGGACCTTGAAGACGAAGTGGGGCAAAAACGTGAAGGCAGTC
                        ttctaat  putative branch site (score: 2)
                                       ttctttgttctgcc  putative PPT
                   attatttctaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtacacggtccagaattgcacctctttgatttcgactttctctttcgtttgccgacaactgtcttgaagaatggctttctgtcgcgttagctctgccgtgctctagtttcacatctctgtggttttgggaagcagtgaagttacggattatttctaataattgagattctttgttctgccagGGATTGCGAAGATATTCTAAAGGCTGCTCTTGAGGGTCAAGACATAGCTCAGGAGGTTTGGACCTTGAAGACGAAGTGGGGCAAAAACGTGAAGGCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA