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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactgaacttcgtttactgttgtgtgataacgtgttggtccattggaatttctgtttgttggggaaatgaaactcattgaagttctgccctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTACGCACGCACGCAATTCCCAAATGTGAAGTACATGGAATATGCTGTGACG

Basic information

species Physcomitrella patens
transcript PP1S46_63V6.4
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_63V6.4 (Physcomitrella patens), 3'ss of exon 13
lower sequence: LOC_Os01g19450.2 (Oryza sativa), 3'ss of exon 15
ttactgaacttcgtttactgttgtgtgataacgtgttggtccattggaatttctgtttgttggggaaatgaaactcattgaagttc---tgccctttgtg-----cagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTACGCACGCACGCAATTCCCAAATGTGAAGTACATGGAATATGCTGTGACG
          |  | ||    | ||   | || ||    | | |  ||||     ||  |   |  |||  |  || |  || |||    ||| ||  ||      |||||||||||  |||| |||||||||||||||||| ||||| | || || || || | ||| || |||||   ||| || |||||||| ||||||||   |
-------gtatgttctatctgtttgct-tgacatgacatttcctaagaatcc---ttcatccag--aatagatttcctcaaatttcactcgcctttcttgattattagGATCAAGAGCAGAGACAACAGAGATAAGAGAGTGCAGCTTCTACAGAAATATGCCCACACACATTTCCCTTCTGTCAAATACATGGAGTATGCTGTCCAG

upper sequence: PP1S46_63V6.4 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 14
--------ttactgaacttcgtttactgttgtgtgataacgtgttggtccattggaatttctgtt-------------tgttggggaaatgaaactcattgaagttctgcc---ctttgtg---cagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTACGCACGCACGCAATTCCCAAATGTGAAGTACATGGAATATGCTGTGACG
        || ||    ||| ||||   ||  |  |||| |  ||   | |||    || || |              ||||    |||| ||| |   ||| | |  |     |||||||    ||| | |||| |   || |||| |||||||||||| |||||  | |||||||  |||||||| || |||||    ||||||||||||||||||||| |    
gtaacgtattccttctgttcattta--attaagcaataaagcattctactatttcccttgctctagctctagctgtagtgttataaaaattaaaatatctgaggcttggttttgctttgtgaaaaagGGTAAAGAATAAGGACAACAAAGATAAGAGAGTAGAGCTACTACAAAAGTTTGCACGCACACATTTCCCTTGCGTGAAGTACATGGAATATGCTATTCAA
















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|37845395|gb|BJ603403.1|BJ603403
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|37844504|gb|BJ602512.1|BJ602512
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|37821565|gb|BJ579631.1|BJ579631
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|37845475|gb|BJ603483.1|BJ603483
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|67698315|gb|BJ958548.1|BJ958548
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|67699841|gb|BJ960074.1|BJ960074
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|208366526|gb|DC955602.1|DC955602
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|37853174|gb|BJ611182.1|BJ611182
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|37843382|gb|BJ601390.1|BJ601390
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|37844166|gb|BJ602174.1|BJ602174
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|162161851|gb|FC338252.1|FC338252
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|37849779|gb|BJ607787.1|BJ607787
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|18337003|gb|BJ169026.1|BJ169026
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
EST: gi|100385297|gb|BY950889.1|BY950889
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGC-ACAG                         GATCAGGAGTCGAGATAAC
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAAC
EST: gi|37826730|gb|BJ584742.1|BJ584742
EST:     GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAG                         GATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA
genomic: GTGGAAAGCATGAAGAAGAAGGGTATCCGTGTTCCTGGAATTGGCCACAGgtaggctctt ... ctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatttctgtttgttggggaaatgaaactcattgaagttctgccctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTACGCACGCACGCAATTCCCAAATGTGAAGTACATGGAATATGCTGTGACG
                                      ttctgcccttt  CT-rich tract
                    aaatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactgaacttcgtttactgttgtgtgataacgtgttggtccattggaatttctgtttgttggggaaatgaaactcattgaagttctgccctttgtgcagGATCAAGAGTCGAGATAACAGAGATAAGAGAGTGGAGCTTTTGCAAAAGTACGCACGCACGCAATTCCCAAATGTGAAGTACATGGAATATGCTGTGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG