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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGGAGGTGGAGTAATCGGGGACATGTGTGGTTATGCTGCTGCTTCTTATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcatgatttcctttaaccccgaacgtatgtttcttccagtatatgataactttttgctcttgcaaccttgtatttttcagcgtcgagattctag...

Basic information

species Physcomitrella patens
transcript PP1S37_309V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_309V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 5'ss of exon 3
ATTGGGAGGTGGAGTAATCGGGGACATGTGTGGTTATGCTGCTGCTTCTTATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttg-aatcatgatttcctttaaccccgaacgtatgtttcttccagtat-atgataactttttgct-cttgcaaccttgtatttttcagcgtcgagattctag
 ||||||||||| || || ||||||||||| |||| ||| |||||| | |  || |||||||||||||| || ||||||||||| || || ||||| |||||   || | ||||||   ||     | |   |  ||| | |  ||  | ||| ||||  |  ||| | || |    | ||                      
GTTGGGAGGTGGCGTTATTGGGGACATGTGCGGTTTTGCAGCTGCTGCGTTCCTGCGTGGTGTCAATTTCATACAGATTCCTACTACTCTGATGGCCCAGgtcctaagcttgatttagattttttactacaattggttacatgtagcttgatgctaacggtgagctgcatgaattactttag---------------------

upper sequence: PP1S37_309V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA01G36890.1 (Glycine max), 5'ss of exon 3
ATTGGGAGGTGGAGTAATCGGGGACATGTGTGGTTATGCTGCTGCTTCTTATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcatgatttcctttaaccccgaacgtatgtttcttccagtatatgataactttttgctcttgc-aaccttgtatttttcagcgtcgagattctag----------------------------------------------------
  | || ||||| || || || ||||||||||| | |||||||||||  |  || |||||||| |||||||| ||||||||||| ||  | ||||| |||||    |  || | |  |  ||          ||| |   |    |||  ||    || | ||||| || ||  ||     ||  ||  ||  | |    |                                                    
TCTTGGTGGTGGTGTGATTGGCGACATGTGTGGCTGTGCTGCTGCTTTGTTCCTACGTGGTGTTAATTTTATTCAGATTCCTACCACTGTGATGGCCCAGgtcttttgctgctcttttaaaaaaatattttcatgatatgtgtt-tattagaccttttgtggctctggctaatgttaatggttctagtctctggctctctgctatctatgttatcccattccctgttcattgggttgtgtattatgttcccag

upper sequence: PP1S37_309V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 3
ATTGGGAGGTGGAGTAATCGGGGACATGTGTGGTTATGCTGCTGCTTCTTATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcatgatttccttt----aaccccgaacgtatgtttcttccagtatatgataa----ctttttgctcttgcaaccttgtatttttcagcgtcgagattctag
  | ||||| || || || || || |||||||| ||||||||||| || || || |||||||||||||| ||||| |||||||| ||  | |||||||||||  | |  | | |||  |     ||   |     ||   |  ||    |  |  | ||     ||||   ||| ||  |  |  ||||    ||   |         
CCTTGGAGGCGGTGTGATAGGCGATATGTGTGGATATGCTGCTGCATCGTACCTACGTGGTGTCAATTTCATCCAAATTCCTACCACTGTTATGGCACAGgtacatttttcacttcactgtaggaatttcttgtctaaaatcattaacatccagaaaaaaggttttttatttctcgctgcaattcatttaattgccctgcag------

upper sequence: PP1S37_309V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 3
ATTGGGAGGTGGAGTAATCGGGGACATGTGTGGTTATGCTGCTGCTTCTTATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgt------tgaatcatgatttcctttaaccccgaacgtatgtttcttccagtatatgataactttttgctcttgcaaccttgtatttttcagcgtcgagattctag
  | || ||||| || || || ||||||||||| | |||||||||| | |  ||||||||||| ||||| || ||||||||||| ||  | |||||||||||      | |||||      | ||| | |  |  | |       || || |   | |    |    |  || |  ||||| | || ||  | |     | |    
CGTTGGTGGTGGTGTTATTGGTGACATGTGTGGATTTGCTGCTGCTGCCTTCCTTCGTGGTGTTAATTTCATTCAGATTCCTACAACTGTAATGGCACAGgtatgtcttaaatcacagcacctttttagctggctcttgctccctttgca-tgcttcaggtgtacaagggctggacaccttct-ttcttaggtgctcctaat----

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|19787988|gb|BQ040695.1|BQ040695
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|162163840|gb|FC340062.1|FC340062
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAA
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAA
EST: gi|162165005|gb|FC342196.1|FC342196
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTT
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTT
EST: gi|100446243|gb|CJ970542.1|CJ970542
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGANCCTCATGGCACAG                         GTANATTCTTCTGTTGG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGG
EST: gi|100375174|gb|BY949195.1|BY949195
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTTGT-GGTGGAAAGACTGGTGTCAACCATCCACTTGAAAA
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCT-GTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAA
EST: gi|100397889|gb|BY953982.1|BY953982
EST:     ATCTTCGTGGTGTCA-TTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|162171473|gb|FC346748.1|FC346748
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|208391322|gb|DC942122.1|DC942122
EST:     ATCTTCGTGGTGTCAATTTTATCCAAAT-CCTACGACCCTCATGGCACAG                         GTAAATTCTNCTGTTG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTG
EST: gi|100409201|gb|BY991896.1|BY991896
EST:     ATCTTCGTGGTGTCAAATTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGGAAGACTGGTGTCAACCATCCACTTGGGAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|208397387|gb|DC908263.1|DC908263
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|162192411|gb|FC368599.1|FC368599
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|208359314|gb|DC939095.1|DC939095
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAN                         GTANATTCTTCTGTNGGTGGAAAGACTGGTGTCAACCATCCACTTGGA
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGA
EST: gi|208369948|gb|DC931511.1|DC931511
EST:     ATCTTCGTGGTGTCAATTTTATCCANATTCCTACGACCCTCATGGCACAG                         GTAAATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAA
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAA
EST: gi|100450979|gb|CJ974536.1|CJ974536
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|208366787|gb|DC940101.1|DC940101
EST:     ATCTTCGTGGTGTCAATTTTATCNANATTCCTACGANCCTCATGGCACAN                         GTAGATTCTTCTGTTGGT
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGT
EST: gi|162191353|gb|FC368149.1|FC368149
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|162214344|gb|FC390063.1|FC390063
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|67718575|gb|BJ968834.1|BJ968834
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
EST: gi|100386492|gb|BY951288.1|BY951288
EST:     ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAG                         GTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG
genomic: ATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAG

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: 35 (upstream exon), 35 (downstream exon)
Score: 22

ATTGGGAGGTGGAGTAATCGGGGACATGTGTGGTTATGCTGCTGCTTCTTATCTTCGTGGTGTCAATTTTATCCAGATTCCTACGACCCTCATGGCACAGgttgaatcat ... gattgtgcagGTAGATTCTTCTGTTGGTGGAAAGACTGGTGTCAACCATCCACTTGGAAAGAATATGATAGGGGCTTTCTATCAACCTCAGTGTGTCCTTGTGGACACCG




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