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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatgaattatgtcataagtttcagcattgatttgccgatggtttgcataggaaaccaatcgcttcctattaattacacgctttcatgattttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTGTGGCGGATCCCAGCTTAG

Basic information

species Physcomitrella patens
transcript PP1S5_248V6.1
intron # 4
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|162204924|gb|FC380606.1|FC380606
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|162229579|gb|FC404860.1|FC404860
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|67696673|gb|BJ956906.1|BJ956906
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|162229580|gb|FC404861.1|FC404861
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|22492592|gb|BU052515.1|BU052515
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|162224698|gb|FC401946.1|FC401946
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|162204923|gb|FC380605.1|FC380605
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|162224697|gb|FC401945.1|FC401945
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|67701119|gb|BJ961352.1|BJ961352
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
EST: gi|67692877|gb|BJ953110.1|BJ953110
EST:     CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAG                         GTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG
genomic: CACAGGATACAAGCTGCGGGTGCTTGCCCAAAACTATCCCACCACACCAGgttcaacgct ... tttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcataggaaaccaatcgcttcctattaattacacgctttcatgattttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTGTGGCGGATCCCAGCTTAG
                                    tttcatgattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatgaattatgtcataagtttcagcattgatttgccgatggtttgcataggaaaccaatcgcttcctattaattacacgctttcatgattttaatgcagGTCTAGCAGTGCGGGATTTTTGGAGCGTCGACGACAATACCGTTGTATTTGTGGCGGATCCCAGCTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG