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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgacgctttacccgcgttcattagagctcatttttttcttttgtgcaagtttgcattggatctctcatctttgttggagttcggaagagtcatattgaacacatcatggtgaattttgaccgatcaatttcgcttttatgccttgatattattctggacgtctcaaaatttgtgaatgcaattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCCCCAGTGCGCTGAAGCGGCAGTTGTTGGGTTCGATCACGAG

Basic information

species Physcomitrella patens
transcript PP1S398_15V6.1
intron # 14
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|162163341|gb|FC339667.1|FC339667
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162208859|gb|FC384995.1|FC384995
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162258983|gb|FC435926.1|FC435926
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162178870|gb|FC354802.1|FC354802
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162187284|gb|FC363234.1|FC363234
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCTGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162156880|gb|FC333034.1|FC333034
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162257810|gb|FC434008.1|FC434008
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162258982|gb|FC435925.1|FC435925
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|67723995|gb|BJ974254.1|BJ974254
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|37829232|gb|BJ587244.1|BJ587244
EST:     TGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: TGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162267683|gb|FC443465.1|FC443465
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162255647|gb|FC431645.1|FC431645
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162171541|gb|FC347843.1|FC347843
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162156881|gb|FC333035.1|FC333035
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162197339|gb|FC372301.1|FC372301
EST:     CAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: CAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|162267682|gb|FC443464.1|FC443464
EST:     GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: GATGGTTACTATTGGTTGACAGGACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
EST: gi|67695932|gb|BJ956165.1|BJ956165
EST:     ATNGTTNCTATTGGTTGACAGGNACGAGTNGNCGATGTCATCAATGTTAG                         TGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC
genomic: ATGGTTACTATTGGTTGACAGG-ACGAGTCGACGATGTCATCAATGTTAGgtcagtgacg ... aattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgccttgatattattctggacgtctcaaaatttgtgaatgcaattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCCCCAGTGCGCTGAAGCGGCAGTTGTTGGGTTCGATCACGAG
      ccttgat  putative branch site (score: 5)
        ttgatattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgacgctttacccgcgttcattagagctcatttttttcttttgtgcaagtttgcattggatctctcatctttgttggagttcggaagagtcatattgaacacatcatggtgaattttgaccgatcaatttcgcttttatgccttgatattattctggacgtctcaaaatttgtgaatgcaattgtacagTGGGCACCGCATTGGTACAGCCGAGGTAGAGTCTGCTCTTGTTTCGCATCCCCAGTGCGCTGAAGCGGCAGTTGTTGGGTTCGATCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC