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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctctatttttatttttgtttttatttttaaattttctgtgtttcacttcttttaccagattctcttgctcttaacaaagcatggtctcactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATCAGAGAGTATAACTCAAAACGCATCTTCAAGGAGCACTTGAAGAGGCTAG

Basic information

species Physcomitrella patens
transcript PP1S63_54V6.2
intron # 1
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|67574237|gb|BJ947061.1|BJ947061
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         TCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|208363504|gb|DC935269.1|DC935269
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         TCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|100356137|gb|BY946215.1|BY946215
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         -----G------G--ACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|100401167|gb|BY990864.1|BY990864
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATC----G---G                         T---TG-CT--AGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|100452688|gb|CJ975394.1|CJ975394
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         TCACTGTCTCCAGGGACANTCCATTCTTGAGCCATG
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATG
EST: gi|18328338|gb|BJ160342.1|BJ160342
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         TCACTGTCTCCAGGGATAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|208376362|gb|DC932272.1|DC932272
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         -----G------G--ACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|162235868|gb|FC412419.1|FC412419
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATC----G---G                         T---TG-CT--AGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|18346689|gb|BJ178734.1|BJ178734
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         TCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|162219070|gb|FC394653.1|FC394653
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATC----G---G                         T---TG-CT--AGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|100426836|gb|BY977387.1|BY977387
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         -----G------G--ACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
EST: gi|100402496|gb|BY954865.1|BY954865
EST:     GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAG                         -----G------G--ACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC
genomic: GATCTTAGAACTACGTGTCTGGTTCTGCTCCTTCGTCAATCGGTTGCTAGgtgagattct ... cactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttcttttaccagattctcttgctcttaacaaagcatggtctcactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATCAGAGAGTATAACTCAAAACGCATCTTCAAGGAGCACTTGAAGAGGCTAG
                                          tctcact  CT-rich tract
                            ttaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctctatttttatttttgtttttatttttaaattttctgtgtttcacttcttttaccagattctcttgctcttaacaaagcatggtctcactgtgcagTCACTGTCTCCAGGGACAATCCATTCTTGAGCCATGGCAAGGAAGAAGATCAGAGAGTATAACTCAAAACGCATCTTCAAGGAGCACTTGAAGAGGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG