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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccccaaaagcattggatcttaaatttttcgggggcgaattttctatttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 3'ss of exon 2
ccccaaaagcattggatcttaaatttttcgggggcgaattttctatttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC---
                   | | | |||      |   ||||  |||   |||| |||||   | || || |        | | || | ||  |      |      |  |    |||||| ||| |  |  | |  || || || || ||||  ||||| | |||||||||||| |||||||||||||||||||| ||    
------------------gtgagtctttttacttctgttttttcattct-tgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT

upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G13920.3 (Arabidopsis thaliana), 3'ss of exon 2
ccccaaaagcattggatcttaaatttttcgggggcgaattttctatttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC---
                       | |||      |   ||||  |||   |||| |||||   | || || |        | | || | ||  |      |      |  |    |||||| ||| |  |  | |  || || || || ||||  ||||| | |||||||||||| |||||||||||||||||||| ||    
----------------------gtctttttacttctgttttttcattct-tgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGGGTATTTATGCT

upper sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 2
ccccaaaagcattggatcttaaatttttcgggggcgaattttctatttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC
                   | | | |||      |   ||||  |||   |||| |||||   | || || |        | | || | ||  |      |      |  |    |||||| ||| |  |  | |  || || || || ||||  ||||| | |||||||||||| ||||||||||||||||        
------------------gtgagtctttttacttctgttttttcattct-tgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGG--------

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC
                           cactaac  putative branch site (score: 1)
                                      tttttgctt  putative PPT
                                     attttt  TA-rich tract