Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctgcggaggatttaaatgttctatcatgtgtcctgactttatgaggattccagaagatatcaattgggctgaaaactacctgctttgaatatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAGAGTCTTATCGAGGCTCATGTAGATGTTAAGACCACGGATAACTACCAGC

Basic information

species Physcomitrella patens
transcript PP1S92_47V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv14s0030g01810.t01 (Vitis vinifera), 3'ss of exon 4
agctgcggaggatttaaatgttctatcatgtgtcctgactttatgaggattccagaagatatcaattgggctgaaaactacctgctttgaatatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAGAGTCTTATCGAGGCTCATGTAGATGTTAAGACCACGGATAACTACCAGC
      |  ||  |   |||     |    | |  |   || || |    | || ||||    ||||||| |     ||   |  ||| ||||  | ||||| ||||| || ||||| ||||||||| ||||  | ||||||||||||||||   | || ||||||||||| ||||||||||| || |||||||||   |
------gtgggcatagcatgacagttagcctttttttttttaattaca--tgcaaaagaggaaaattggggttt---ctcattttttttaataatttcagGGAATGGACTTTACAACAGACAAGCTGAGGTCTTTGGTGCGCAAGTGGCAGACATTGATTGAGGCTCATGTGGATGTTAAGACAACAGATAACTACACCC

upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EDP08964 (Chlamydomonas reinhardtii), 3'ss of exon 4
agctgcggaggatttaaatgttctatcatgtgtcctgactttatgaggattccagaagatatcaattgggctgaaa-actacc-tgctttgaat-atctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAGAGTCTTATCGAGGCTCATGTAGATGTTAAGACCACGGATAACTACCAGC
  |  | | |  ||   |        |  | ||||||  |      | | | ||     |  |   ||| | |  |   |  | |||  |     |||  ||||| ||||| || || || ||||||||||| || || || |||||||||||||  || |||||||| || || || || |||||||||||   ||||   |
-cccacagcgcgttaccagcagggggcgggggtcctgtgtaggcaggcaatgcaccgattgac--ctggcccgccatgttgtcgtgccctctgcgatccgcagGGCATGGACTTCACTACGGACAAGCTGCGCTCGCTGGTCCGCAAGTGGCAGACCCTGATCGAGGCGCACGTGGACGTGAAGACCACGGACGGCTACACCC
















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|67571386|gb|BJ944210.1|BJ944210
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGC
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGC
EST: gi|37844503|gb|BJ602511.1|BJ602511
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18347427|gb|BJ179473.1|BJ179473
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18347038|gb|BJ179084.1|BJ179084
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|100450921|gb|CJ974507.1|CJ974507
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|37847269|gb|BJ605277.1|BJ605277
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18373995|gb|BJ205573.1|BJ205573
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162261198|gb|FC437215.1|FC437215
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162185712|gb|FC361566.1|FC361566
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|6167400|gb|AW145664.1|AW145664
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|37851788|gb|BJ609796.1|BJ609796
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162216969|gb|FC393087.1|FC393087
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|100360481|gb|BY984147.1|BY984147
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|208360419|gb|DC950032.1|DC950032
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|67694711|gb|BJ954944.1|BJ954944
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162216968|gb|FC393086.1|FC393086
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|37826206|gb|BJ584218.1|BJ584218
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|19777641|gb|BQ039208.1|BQ039208
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18351838|gb|BJ183890.1|BJ183890
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|19788665|gb|BQ040844.1|BQ040844
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162217884|gb|FC393880.1|FC393880
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18345407|gb|BJ177450.1|BJ177450
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|208372026|gb|DC936226.1|DC936226
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG

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), 32 (downstream exon)
Score: 38

CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAGAGTCTTATCGAGGCTCATGTAGATGTTAAGACCACGGATAACTACCAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggattccagaagatatcaattgggctgaaaactacctgctttgaatatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAGAGTCTTATCGAGGCTCATGTAGATGTTAAGACCACGGATAACTACCAGC
             atatcaatt  TA-rich tract