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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattaaacccagtaagttgattcacactcattaatagtactgcccagttccgttagctttgtcattttttaatccaattatctcgcattttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTATATGCAAATGGATGGAGAGCCGTGGATGCAACCAATGGGTTCGCATCTTG

Basic information

species Physcomitrella patens
transcript PP1S213_133V6.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S213_133V6.2 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA18G22370.1 (Glycine max), 3'ss of exon 4
----ttgattaaacccagtaagttgattcacactcattaatagtactgcccagttccgttagctttgtcattttttaatccaattatctcgcattttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTATATGCAAATGGATGGAGAGCCGTGGATGCAACCAATGGGTTCGCATCTTG
||||| | | | | || | ||| | || ||| |||| | | |||| ||| | | || | | | | | | | |||| || || | | || ||| ||| || | || | || | |||||||||||||||||| ||||||| ||||||||| | | | |
aactttgatcagaactatta---ttattgttataaatatatacgactgttatcattagcatcatttggcatgtgtgaaattgaatgtagag-gtctaattttagGCAACAGCTATTCGATTGGAAGTCAGAGGTGGTGAATGGAAAGATGCATTTATGCAAATGGATGGAGAACCGTGGAAACAACCAATGAGCAAGGACTTCT
















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|37824667|gb|BJ582733.1|BJ582733
EST:     ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAA                         GCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
genomic: ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAAgtaagcgttt ... tttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
EST: gi|37839304|gb|BJ597312.1|BJ597312
EST:     ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAA                         GCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
genomic: ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAAgtaagcgttt ... tttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
EST: gi|37837212|gb|BJ595220.1|BJ595220
EST:     ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAA                         GCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
genomic: ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAAgtaagcgttt ... tttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
EST: gi|67695915|gb|BJ956148.1|BJ956148
EST:     ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAA                         GCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
genomic: ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAAgtaagcgttt ... tttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
EST: gi|37844060|gb|BJ602068.1|BJ602068
EST:     ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAA                         GCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
genomic: ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAAgtaagcgttt ... tttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
EST: gi|37852409|gb|BJ610417.1|BJ610417
EST:     ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAA                         GCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
genomic: ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAAgtaagcgttt ... tttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
EST: gi|162247614|gb|FC420552.1|FC420552
EST:     ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAA                         GCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT
genomic: ATTCGGCTTTTGTTCTCCTTGAAGTTTCCACTGCTGTTCGTCTTTGTCAAgtaagcgttt ... tttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagttccgttagctttgtcattttttaatccaattatctcgcattttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTATATGCAAATGGATGGAGAGCCGTGGATGCAACCAATGGGTTCGCATCTTG
                       ttttaat  putative branch site (score: 3)
 ttttgctcc  putative PPT
 attttttaatccaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattaaacccagtaagttgattcacactcattaatagtactgcccagttccgttagctttgtcattttttaatccaattatctcgcattttgctccagGCCGAGGCAATCAAAATTGAGCTCAATGGTCATGCGCGAAAGAAAGCTTATATGCAAATGGATGGAGAGCCGTGGATGCAACCAATGGGTTCGCATCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA