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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccatttttttgtgatcgaataaggccatatcgatatttcttttgttgtcatatcttttatttagactgtctgatttagacactccgtcgcttgctcttgtcacctacttttgtttttctgtggaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC

Basic information

species Physcomitrella patens
transcript PP1S205_25V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 4
---gtatgccatttttttgtgatcgaataaggccatatc--gatatttcttttgttgt-catatctt-ttatttaga-------ctgtctgatttagacact-ccgtcgcttgctcttgtcacc-tacttttgtttttctgtggaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
     |   ||  || |||    | |    | | ||     | | | | |||  ||||     |||  || | | |         ||       | ||   |   || |||| || | | ||   || |    ||  | ||| |      ||||||| |||||||| |||||||||||||||||||| ||||| || |||||||||||  | |||||||| ||||||||| | || || ||||| || |||  
gtcagaattcagattattgatcccaatcttgacgatgctctggtgtctatttctttgtgtgcctctagttgtgtgggagggtagttgctcaggattgatgttatggtggcttcctatggacataatattcacattaatttgttg------cagAGAAGGATTGGGATGATATCAAGTTTGGAGTGGATAACAAAGTTGACTTTTATGCTGTTTCCTTTGTTAAGGATGCTGAAGTTGTTCATGAGCTGAAGAA

upper sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 4
--------gtatgccatttttttgtgatcgaataaggccatatcga-tatttcttttgttgtcatatcttttatttaga-----ctgtctgatttagacactccgtcgcttgctcttgtcacctacttttgtttttctgtggaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
          |    ||   |          | || ||  ||  |  |||||||||   || | |   ||   |           ||       | ||   |  |  | || |   ||      |  ||    ||  | ||     | ||||||| |||||||| |||||||||||||||||||| ||||| || ||||| |||||  | |||||||| ||||||||| | || || |||||||| |||  
gtcagaattcagattatgaatcccaatcttgacaatgctctagtgtctatttctttgtgtgccttgagttgcgtgggagggtagttgctcaggattgatgttatggtggtttcctatggacataatattcacattaatttg----ttgcagAGAAGGATTGGGATGATATCAAGTTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCCTTTGTTAAGGATGCTGAAGTTGTTCATGAACTGAAGAA

upper sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
--------gtatgccatt-tttttgtgatcgaataaggcc---atatcga--tatttcttttgt-tgtcatatcttttatttag--actgtctgattta-gacactccgtcgcttgct--cttgtcacctacttttg-tttttctgtggaat--ctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
         |    |||| ||  | |  | || |         || |  |   ||||||| |   || |    | | | ||| |  |||| |  ||    ||   |       ||| |   ||  ||   || | |  | ||| ||| || |  || ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||| |||||  | || ||||| |||||||| || || || |||||||| |||  
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA

upper sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 4
-----------gtatgccattttt-ttgtgatcgaataaggccatatcgat--atttcttttgt-tgtcatatcttttatttag--actg---tctgatttagacactccgtcgcttgctcttgtcacctacttttg-tttttctgtggaat--ctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
           |  |   |||| | |  ||||    |      || |   |  ||||||| |   || |    | | ||||| |  ||||    |||  | ||       ||    |    ||  ||   || | |  | ||| ||| || |  || ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||| |||||  | || ||||| || ||||| || || || |||||||| |||  
gttagattccggattattatttctatcttgattatttcttttaatgtttgtccatttcttctacatgcctctccatatatttgggtactgacaactgggtgagggttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAAGATGCACAAGTAGTTCATGAACTGAAGAA

upper sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgccatttttttgtgatcgaataaggccatatcgatatttcttttgttgtcatatcttttattta-gactgtctgatttagacactccgtcgcttgctcttgtcacctacttttgtttttctgtggaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
||  |   ||| | | |   |   |     | | |   | || |||| ||||   | |    |||||| | |||   ||| |    |||| |  ||||  | ||      |    || ||||  ||  |      ||||||| || ||||| ||||| || ||||||||||| ||||| || |||||||||||  | ||||||||||| |||||||| || || || ||  | |||  
gttcgaattttctgtttaccctctttttcactttttcttgttgctttggttgaagtgttgcatatttaagtctgaaagatct---tactctgatgcttattttt------tgtaattattttcttgccg------cagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA

upper sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv02s0012g01170.t01 (Vitis vinifera), 3'ss of exon 4
----------gtatgccatttttttgtgatcgaataaggccatatcgatatttctt------ttgttgtcatat--cttttatttagactgtctgatttagacactccgtcgcttgctcttgtcacctacttttgt----ttttctgtggaatctc--cagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
          || |   || |||||   |     | |     | |   |||||         ||| | | || |  |||||| ||  | |     | |||     |   |   |||        | | | | || |    ||     ||  || ||  |||| ||||| |||||||||||||||||||||||||| ||| | || || || |||||  | |||||||| || |||||| | ||||| |||||  | ||   
gttatcttttgt-tcttatgttttttctaataggtgattttctgtttctattttccacgaagttgatatgatgtttcttttacttttatttgtctacttacgtgttatttgaattgtaaaaaatatccaatcttttcccattactcatgtcatttcaacagACAAAGACTGGGAAGATATCAAGTTTGGAGTGGACAACCAAGTTGATTTCTATGCTGTTTCCTTTGTGAAAGATGCTGAAGTGGTCCATGAGTTGAAAGA

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|162153879|gb|FC330010.1|FC330010
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|100407600|gb|BY991774.1|BY991774
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162179280|gb|FC356229.1|FC356229
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162178857|gb|FC354789.1|FC354789
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCANGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162156500|gb|FC332108.1|FC332108
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|208360056|gb|DC939332.1|DC939332
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162278586|gb|FC454048.1|FC454048
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162177062|gb|FC353115.1|FC353115
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162179457|gb|FC355457.1|FC355457
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162159393|gb|FC334661.1|FC334661
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
EST: gi|162181032|gb|FC358686.1|FC358686
EST:     TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAG                         AGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT
genomic: TCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTT

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: 34 (upstream exon), 34 (downstream exon)
Score: 17

CATGAGGAAGTTCTCTGTGAGGTAGTGGACGGGGGTGAACTGAAGTCTCGTCGTCATCTCAACGTGCGTGGCAAGAGTGCCACTCTACCCTCCATTACAGgtatgccatt ... gaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacactccgtcgcttgctcttgtcacctacttttgtttttctgtggaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
                                                tctcc  CT-rich tract
                              ttttgttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccatttttttgtgatcgaataaggccatatcgatatttcttttgttgtcatatcttttatttagactgtctgatttagacactccgtcgcttgctcttgtcacctacttttgtttttctgtggaatctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG