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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_1V6.1
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|67709710|gb|BJ965526.1|BJ965526
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67719323|gb|BJ969582.1|BJ969582
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|100415489|gb|BY992868.1|BY992868
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18347993|gb|BJ180040.1|BJ180040
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67717840|gb|BJ968099.1|BJ968099
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18346096|gb|BJ178139.1|BJ178139
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162186231|gb|FC362163.1|FC362163
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18330779|gb|BJ162785.1|BJ162785
EST:     ATGCTCGCCAATATGACGCCNANATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: ATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18347116|gb|BJ179162.1|BJ179162
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|208387260|gb|DC933011.1|DC933011
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|100396855|gb|BY953861.1|BY953861
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|208348012|gb|DC905335.1|DC905335
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162155800|gb|FC331829.1|FC331829
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|100397158|gb|BY972359.1|BY972359
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67702772|gb|BJ963005.1|BJ963005
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67717313|gb|BJ967572.1|BJ967572
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162267873|gb|FC444474.1|FC444474
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162189204|gb|FC366726.1|FC366726
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|67703834|gb|BJ964067.1|BJ964067
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162163659|gb|FC339764.1|FC339764
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|162193356|gb|FC370948.1|FC370948
EST:     GAAGGGACTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18357312|gb|BJ189371.1|BJ189371
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
EST: gi|18345348|gb|BJ177391.1|BJ177391
EST:     GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATAT                         CTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA
genomic: GAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 33 (downstream exon)
Score: 28

CAGCGAAGTAGTATGGCTGGATCTGCACCCGAAGGGTCTCAGTTCGATGCTCGCCAATATGACGCCAAGATGGAGAATATgtaagagcgt ... ttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATAC
                           cactaac  putative branch site (score: 28)
                                      tttttgctt  putative PPT
                                     attttt  TA-rich tract