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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctttctcctccttgatttaatttctctccgcgcctaccagtgttgctcaagcagttttgtcttgaacgttagacaatttaaatccttggttgacttctgacggcaagttgggtgtactcag

Basic information

species Physcomitrella patens
transcript PP1S1_527V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA09G28100.1 (Glycine max), 5'ss of exon 6
TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctttctcctccttgatttaatttctctccgcgcctaccagtgttgctcaagcagttttgtcttgaacgttagacaatttaaatccttggttgacttctgacggcaagttgggtgtactcag
 | ||||||||||||||||| ||||||||||| ||||| |||||||||||||||| ||||   || | ||| || ||| ||||  |               | ||| | |  |    |    ||  ||||   ||       |  ||    |    ||  |   ||| |||  || |                                
CTTGGAGCCAATGCTATTTTGGCAGTGTCACTTGCTGTCTGCAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtga------------ggtttcagtaataaaagtatttataagtgaaacttgtattctcatggtccgctt-ttgtattgttttaatttttag--------------------------------

upper sequence: PP1S1_527V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 6
TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctttctcctccttgatttaatttctctccgcgcctaccagtgttgctcaagcagttttgtcttgaac-gttagacaatttaaatccttggttgacttctgacggcaagttgggtgtactcag
 | ||||| ||||||||||| ||||||||||| ||||| || ||||||||||||| ||||   || | ||| || ||| ||||  |     | |     | |   || ||  | || | |  | |  ||||| |||| |   | |  | |||||  |||  |   ||| |                                        
CTTGGAGCTAATGCTATTTTGGCAGTGTCACTTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtgaggtttttcagtagtaatagttcttatctgtgaat-cttgtgtt-ctcatgt--tctgcttttgaattgttttattttttcag---------------------------------------
















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|67717547|gb|BJ967806.1|BJ967806
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|100387077|gb|BY951476.1|BY951476
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|67717549|gb|BJ967808.1|BJ967808
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|18370202|gb|BJ201804.1|BJ201804
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|208359629|gb|DC934616.1|DC934616
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|208357716|gb|DC902282.1|DC902282
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|208384682|gb|DC907127.1|DC907127
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|18361801|gb|BJ193868.1|BJ193868
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|100369601|gb|BY948562.1|BY948562
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|100409225|gb|BY991908.1|BY991908
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|100438709|gb|BY961762.1|BY961762
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|208394185|gb|DC933853.1|DC933853
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|100428551|gb|BY977864.1|BY977864
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAA
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAA
EST: gi|100365044|gb|BY966782.1|BY966782
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|18365720|gb|BJ197797.1|BJ197797
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAA
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAA
EST: gi|100448364|gb|CJ972663.1|CJ972663
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|18374449|gb|BJ206027.1|BJ206027
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|208378006|gb|DC906935.1|DC906935
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|100440922|gb|BY962410.1|BY962410
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
EST: gi|100401183|gb|BY990872.1|BY990872
EST:     TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAG                         CACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC
genomic: TGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCC

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: 23 (upstream exon), 30 (downstream exon)
Score: 17

TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctt ... gtgtactcagCACATTGCCAACCTGGCTGGCAACAAGGAAATTGTGATGCCAGTGCCTGCCTTCAACGTGATCAATGGTGGATCTCATGCTGGCAACAAGCTCGCCATGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGGAGCCAATGCTATTTTAGCAGTGTCACTGGCTGTGTGCAAGGCTGGTGCTGGAGTGTTAAAGACTCCACTTTACCAGgttagctctttctcctccttgatttaatttctctccgcgcctaccagtgttgctcaagcagttttgtcttgaacgttagacaatttaaatccttggttgacttctgacggcaagttgggtgtactcag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA