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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattgaatcaatcagtctttaggattagtttttgtctatcagaaatgaatttcgactagggtttttgtgtgttgctattgatttggcctatatgtgcagGGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACCCACAACTTTCACAGGAAAGCATTACGGAGGAGCTGTTGATGCAGTTTTC

Basic information

species Physcomitrella patens
transcript PP1S61_322V6.1
intron # 21
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|162196273|gb|FC374355.1|FC374355
EST:     TTACCACCATTGGTAGACTGTGCCATGACTGGCATAACTATTCAACACAG                         GGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACC
genomic: TTACCACCATTGGTAGACTGTGCCATGACTGGCATAACTATTCAACACAGgtacttttat ... atatgtgcagGGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACC
EST: gi|162196274|gb|FC374356.1|FC374356
EST:     TTACCACCATTGGTAGACTGTGCCATGACTGGCATAACTATTCAACACAG                         GGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACC
genomic: TTACCACCATTGGTAGACTGTGCCATGACTGGCATAACTATTCAACACAGgtacttttat ... atatgtgcagGGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACC
EST: gi|162244564|gb|FC420111.1|FC420111
EST:     TTACCACCATTGGTAGACTGTGCCATGACTGGCATAACTATTCAACACAG                         GGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACC
genomic: TTACCACCATTGGTAGACTGTGCCATGACTGGCATAACTATTCAACACAGgtacttttat ... atatgtgcagGGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatttcgactagggtttttgtgtgttgctattgatttggcctatatgtgcagGGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACCCACAACTTTCACAGGAAAGCATTACGGAGGAGCTGTTGATGCAGTTTTC
                               tattgat  putative branch site (score: 3)
                               tattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattgaatcaatcagtctttaggattagtttttgtctatcagaaatgaatttcgactagggtttttgtgtgttgctattgatttggcctatatgtgcagGGAGGCATGTCGTTCAATTTTGACCTTTTTCCAAGATATCTTGGATGTACCCACAACTTTCACAGGAAAGCATTACGGAGGAGCTGTTGATGCAGTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT