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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcctgttgatgaactgtcgtggaaacttgatgaattttggtttggaatagtcgacctgcaatgaccatgttttcgtatcgtgtgatacttttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAGGTTCCCCATATTCAG

Basic information

species Physcomitrella patens
transcript PP1S414_24V6.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S414_24V6.1 (Physcomitrella patens), 3'ss of exon 21
lower sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 17
atcctgttgatgaactgtcgtggaaacttgatgaattttggtttggaatagtcgacctgcaatgac-catgttttcgtatcgtgtgatac-ttttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAGGTTCCCCATATTCAG
| |||| || | ||| | | | | ||| | | || | | |||| |||||||| |||| ||||| |||||||| |||||| |||||||||||| ||||| | || || || ||
------------------------------gtttgctttgcttcttctcaatcgtctcgtctcgtttcgtgtgctaggattttaactagcgtttttcatcagGCTGTTCTTCGCTCCTTGTATGCCTACTTTGCGGACAAACCACTGAAAGAAATCCCACACATCGAG
















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|162183439|gb|FC359562.1|FC359562
EST:     TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAA                         GCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
genomic: TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAAgtaagtacta ... tttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
EST: gi|162258015|gb|FC434109.1|FC434109
EST:     TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAA                         GCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
genomic: TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAAgtaagtacta ... tttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
EST: gi|37843086|gb|BJ601094.1|BJ601094
EST:     TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAA                         GCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
genomic: TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAAgtaagtacta ... tttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
EST: gi|37840559|gb|BJ598567.1|BJ598567
EST:     TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAA                         GCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
genomic: TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAAgtaagtacta ... tttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
EST: gi|67698398|gb|BJ958631.1|BJ958631
EST:     TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAA                         GCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
genomic: TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAAgtaagtacta ... tttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
EST: gi|208397007|gb|DC924685.1|DC924685
EST:     TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAA                         GCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG
genomic: TTGTAGAGCTTGAGAGGCAGCGCTCACCAGTGGTGGTAATTGCACATCAAgtaagtacta ... tttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatagtcgacctgcaatgaccatgttttcgtatcgtgtgatacttttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAGGTTCCCCATATTCAG
                                           cttttccatc  CT-rich tract
 atactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcctgttgatgaactgtcgtggaaacttgatgaattttggtttggaatagtcgacctgcaatgaccatgttttcgtatcgtgtgatacttttccatcagGCAATTCTCCGCTCATTGTATGCATACTTTATGGACAAACCACTCAAAGAGGTTCCCCATATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG