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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttattaacaattttcgtttctatcttttaattcatcataccctcgaattttgtcatgctttcttcagattataaatgcagctcgtttaaataaact...

Basic information

species Physcomitrella patens
transcript PP1S168_70V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S168_70V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 1
-------GTCTTGTAAG--ATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttattaacaattttcgtttctatcttttaattcatcataccctcgaattttgtcatgctttcttcagattataaatgcagctcgtttaaataaact----
         |  |  ||  ||||  || || || ||          || || |  ||  ||||||||||||||||||| || |||||||| ||||||||||| | |  |  | ||||  | | || || | ||     |||| |  |  | ||||     |  || | |   |        |   || |  ||  | |      
TTCAGGTAGCCAGCCAGTCATGGTGCTCTTCAATGTTTCACGCGTAGAGACCACTCCCTTCGATGGCCAGAAGCCTGGAACCTCTGGTCTCCGCAAGAAGgttccttatctcgattt--gatcctttcctctatcaattcatgcttt--agtttttctgagaattgtactactcgctggatcttgtcttcaaatcatatcttct

upper sequence: PP1S168_70V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 1
-------GTCTTGTAAG--ATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttattaacaattttcgtttctatcttttaattcatcataccctcgaattttgtcatgctttcttcaga-ttataaatgcagctcgtttaaataaact----
         |  |  ||  ||||  || || || ||          || || |  ||  ||||||| ||||||||||| || |||||||| ||||||||||| |||||    | |||    ||   ||| | ||| |||      ||  | ||||  |  |||   | ||   ||     |   | || | | |  |   |    
GGTAGCCAGCCAGCCAGCCATGGTGCTCTTCAATGTTTCACGCGTTGAGACCACTCCCTTCGATGGACAGAAGCCTGGAACCTCTGGTCTCCGCAAGAAGgtccttatctcgattttatcctttcctctatcaatccatg-----ctttagtttttccgcgctcgatacattctttcttcttttgttcttctgacgattgtacta
















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|208391163|gb|DC942075.1|DC942075
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18360636|gb|BJ192699.1|BJ192699
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|100386703|gb|BY970244.1|BY970244
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|162194861|gb|FC370525.1|FC370525
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18345963|gb|BJ178006.1|BJ178006
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18359483|gb|BJ191544.1|BJ191544
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|100405914|gb|BY991447.1|BY991447
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|162162825|gb|FC338087.1|FC338087
EST:     GCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: GCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18365419|gb|BJ197494.1|BJ197494
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|162181557|gb|FC358171.1|FC358171
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18346813|gb|BJ178858.1|BJ178858
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18369304|gb|BJ201390.1|BJ201390
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGANCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18367821|gb|BJ199904.1|BJ199904
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCANGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18366141|gb|BJ198219.1|BJ198219
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18371368|gb|BJ202970.1|BJ202970
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|100368990|gb|BY984972.1|BY984972
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|67575939|gb|BJ948763.1|BJ948763
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|162193559|gb|FC370462.1|FC370462
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|208384123|gb|DC911259.1|DC911259
EST:     CTAAGCCGATCGATGGCCANAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|162164264|gb|FC342079.1|FC342079
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
EST: gi|18360603|gb|BJ192666.1|BJ192666
EST:     CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG                         GTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC
genomic: CTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttatta ... atctgtgcagGTGACAGTATTCAAGCAAGAGCATTATCTTGCCAACTTTGTTCAGGCTACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAGgtgcttattaacaattttcgtttctatcttttaattcatcataccctcgaattttgtcatgctttcttcagattataaatgcagctcgtttaaataaact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG