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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgtttctatccatcatcgctattatcatcatgcactttctaaagcctccatatttggatccaacattttgatatgtcagtgctaccactgctt...

Basic information

species Physcomitrella patens
transcript PP1S383_1V6.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 2
CGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgtttctatccatcatcgctatt--atcatcatgcactttctaaag-----cctccatatttggatccaacattttgatatgtcagtgctaccactgctt--------------------------------------------------------------------------------------
     ||  |||||||| || ||||||||||| || || ||||||||||| |||||||| || |||||| |  |  |||| |        |  |    || | |  |  ||    ||||  |  ||  ||     |||  |||||   ||   |  | ||  |    |  |  ||  | | | |                                                                                      
TTTGCTATCATGGCTGGGTCGGCACCCGAAGGATCACAATTCGATGCTCGTCAATATGATGCTAAGATGAATGAGTTgtaggtttccccttcccttagatggatgcttaatagagatgccatggcttgagatatgcctttatattataataatatgtattagtgataccatcttattatttcatgtgtaatgcctacctgtgaactgtgatacatccatgcctagaagaattatatgctcattcttggttttatgttttcatgggaccag
















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|100415489|gb|BY992868.1|BY992868
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67719323|gb|BJ969582.1|BJ969582
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18357312|gb|BJ189371.1|BJ189371
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18330779|gb|BJ162785.1|BJ162785
EST:     ATGCTCGCCAATATGACGCCNANATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: ATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162189204|gb|FC366726.1|FC366726
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|100396855|gb|BY953861.1|BY953861
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67717313|gb|BJ967572.1|BJ967572
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67717840|gb|BJ968099.1|BJ968099
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162186231|gb|FC362163.1|FC362163
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|208387260|gb|DC933011.1|DC933011
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18346096|gb|BJ178139.1|BJ178139
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162193356|gb|FC370948.1|FC370948
EST:     GAAGGGACTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67702772|gb|BJ963005.1|BJ963005
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162155800|gb|FC331829.1|FC331829
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67709710|gb|BJ965526.1|BJ965526
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162163659|gb|FC339764.1|FC339764
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|208348012|gb|DC905335.1|DC905335
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|100397158|gb|BY972359.1|BY972359
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162267873|gb|FC444474.1|FC444474
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18347993|gb|BJ180040.1|BJ180040
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18345348|gb|BJ177391.1|BJ177391
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18347116|gb|BJ179162.1|BJ179162
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgtttctatccatcatcgctattatcatcatgcactttctaaagcctccatatttggatccaacattttgatatgtcagtgctaccactgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA