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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttgcttctgaacaaggattgttgtacgaatcttttgaaatggttagtccaaagccactagcaattcatgaaagctatggtggaaaagctagtgcatattgaagtgactttttgttatcatccaactagcccatccaattgtcacttggccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCTACCAGCGTAAAATTTGAGATATGGGACACTGCAGGTCAAGAACG

Basic information

species Physcomitrella patens
transcript PP1S38_328V6.3
intron # 4
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|162152196|gb|FC328175.1|FC328175
EST:     GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAG                         GTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
genomic: GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAGgttagtttgc ... ccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
EST: gi|208397759|gb|DC911996.1|DC911996
EST:     GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAG                         GTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
genomic: GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAGgttagtttgc ... ccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
EST: gi|7648245|gb|AW739228.1|AW739228
EST:     GGCAATTCGACCCCTCGTCCAAG                         GTGACGGTTGGCGCGTCGTTTCTTTCTCATACAATTACATTGAAAGATTCT
genomic: GGCAATTCGACCCCTCGTCCAAGgttagtttgc ... ccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
EST: gi|100370853|gb|BY948549.1|BY948549
EST:     GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAG                         GTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
genomic: GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAGgttagtttgc ... ccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
EST: gi|162267081|gb|FC443312.1|FC443312
EST:     GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAG                         GTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
genomic: GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAGgttagtttgc ... ccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT
EST: gi|100440896|gb|BY962384.1|BY962384
EST:     GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAG                         GTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAGGATTCT
genomic: GTTGCATTGTCTTACGGTTTGTGCGTGGGCAATTCGACCCCTCGTCCAAGgttagtttgc ... ccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgactttttgttatcatccaactagcccatccaattgtcacttggccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCTACCAGCGTAAAATTTGAGATATGGGACACTGCAGGTCAAGAACG
     ttttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttgcttctgaacaaggattgttgtacgaatcttttgaaatggttagtccaaagccactagcaattcatgaaagctatggtggaaaagctagtgcatattgaagtgactttttgttatcatccaactagcccatccaattgtcacttggccgtgtgcagGTGACGGTTGGCGCGTCGTTTCTTTCTCAGACAATTACATTGAAAGATTCTACCAGCGTAAAATTTGAGATATGGGACACTGCAGGTCAAGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC