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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA

Basic information

species Physcomitrella patens
transcript PP1S264_34V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os05g28280.1 (Oryza sativa), 3'ss of exon 6
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgca--gCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
                  |  | |  || |  || | ||||||      |    | ||    |    |    || |  |||  |     || ||| |||  ||||||||| || |||||||||||||||||  | || ||||| ||||| ||||||||||||||| |||| ||||| ||||| || ||||| ||||| || |
------------------gtgagaatagctgcttttatttgaa---ggattgtcttctgtttgctttttttttttacatttttttttaattacgacgcacagCCCAAGTTATTGGATGAGAAGCAGACCACCATCTACAAGAGAGCTGTAGACAAGAATTATCACTTGAAGATGAAAGCATCTAGGTTCATTTTCAGTGAGA

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G388234_T01 (Zea mays), 3'ss of exon 2
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA------
                   |||    |  | ||| | |||| |  | |      |  ||        |   |  |   |||| |      | |    || |||||||| || |||||||||||||||||  | || || |||||||| |||||||| ||| ||||||| ||||| |||||||  || || ||||| ||||      
-------------------gtaagaaattttgtt-tttttgcatgtgatgcttcttttttttccatgtatgaccacattttcgttgaatattcatgccaacccaagTTATTGGATGAGAAGCAGACCACTATCTACAAAAGGGCTGTAGACAAGAACTATAACCTGAAGATGAAAGCATCAACGTTTATTTTCAGTGAAATCAGCC

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AC233895.1_FGT001 (Zea mays), 3'ss of exon 5
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
                      ||   |||  |  | |||| |  |  |||      ||     |  |   || |    ||  |      | |   |||||||||||| || |||||||| ||||||||  | || || ||||| || ||||||||||||||| |||| ||||| || ||||| || || ||||| || |
---------------------gtaagcgattctgttatttgcatatg-ctgctcctttttttccctgtttgatcacgtctttgttgaatattcatggcagCCCAAGTTATTGGATGAGAAACAGACCACCATCTACAAAAGGGCCGTAGACAAGAATTATCACTTGAAGATGAAAGCGTCAAGGTTTATTTTCAGTGAGA

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G133884_T01 (Zea mays), 3'ss of exon 2
-taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggc--attaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
 |   ||  |    || |||   ||  | ||  |  | |||      |  ||| |    |     ||||| |  || |   |||| |      | |    ||||||||||| || |||||||||||||||||  | || || | || ||| |||||||||||| || |||| ||||| |||||||| || || ||||| ||||
atgtgtttctacgtttttag---taagaaattctgttttttttttgcatgtgatgcttcttttttccatgtctgatcacattttcgtagaatattcatgccagCCCAAGTTATTGGATGAGAAGCAGACCACTATCTACAAAATGGTTGTAGACAAGAATTATAACTTGAAGATGAAAGCATCAAGGTTTATTTTCAGTGAAA

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G440820_T01 (Zea mays), 3'ss of exon 1
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaag-tccttcaggaccatggc--attaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA-
  ||  || |     |  || |    ||| | |  | |||      |  ||| | | |||     ||||| |  |  |   |||| |      | |    ||||||||||| || ||||||||  |||||||  | || || |||||||| |||||||| ||| ||||||||||||| |||||||| || || ||||  |||| 
--ccagcactgggg-aggggaaggtaagaaattcttttttttttgcatgtgatgcttctttttttccatgtctgaccacattttcgttgaatattcatgccagCCCAAGTTATTGGATGAGAA-TAGACCACTATCTACAAAAGGGCTGTAGACAAGAACTATAACCTGAAAATGAAAGCATCAAGGTTTATTTTCAATGAAAT

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G18500.1 (Glycine max), 3'ss of exon 6
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
          || ||  |  |||| ||   |  ||| |   |   |    ||  |  | || ||  ||    | ||| ||||||      ||   ||||||| ||| |||| |||||||||||||| ||  | |||||||||||||| ||||||| ||||||| |||| ||||| || || || ||||| ||||| ||||
---------gtagtt-caattatatca---acatatttactagtatggtagagcttatgcatgat-ataaagtaaat-tttcat------tctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G19310.1 (Glycine max), 3'ss of exon 3
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
          || ||  |  |||| ||   |  ||| |   |   |    ||  |  | || ||  ||    | ||| |||||||      |   ||||||| ||| |||| |||||||||||||| ||  | |||||||||||||| ||||||| ||||||| |||| ||||| || || || ||||| ||||| ||||
---------gtagtt-caattatatca---acatatttactagtatggtagagcttatgcatgat-ataaagtaaat-tttcatc------ctcttgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATCTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAAA

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA18G43390.1 (Glycine max), 3'ss of exon 6
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
                  ||||   ||  ||  |     || |    | |   ||    |     ||||  |  ||   |  ||     |||   ||||||| ||| |||| |||||||||||||| ||  | |||||||||||||| ||||||| ||||||| |||| ||||| || || || ||||| ||||| ||| 
------------------ggtaggtcaattatattaacatgtatactagtatggtagagcttatgcatgata--aaaagtaaattttcattctcttgcaGCCTAAGCTGTTGGATGAGAAGCAGACAACTATTTATAAGAGGGCTGTTGACAAGAGTTATCACTTGAAGATGAAAGCGTCTAGGTTCATTTTCAGTGAA-

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA01G29420.1 (Glycine max), 3'ss of exon 6
taccttcatttaattataggtatagcagatagttatctttgaacttaactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
          |||||   ||| |     |||  ||| |    |  | |   |  || | |    || | || ||| |       || | |     ||||||| ||| |||| |||||||||||||| ||  | |||||||| ||||| |||||||  |||||  | || ||||| ||||| || ||||| ||||| ||||
---------gtaattt--ggttttattaata--tatttactgatatgatgca--tcttcctaatcctttgc-ttagtaaaattccaatctct---tgcagCCTAAGCTGTTGGATGAGAAGCAGACAACTATTTATAAGAGAGCTGTTGACAAGAGCTATCATTTAAAGATGAAAGCATCTAGGTTCATTTTCAGTGAAA

upper sequence: PP1S264_34V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv06s0004g06870.t01 (Vitis vinifera), 3'ss of exon 6
---taccttcatttaattata-ggtatagcagatagttat--ctttgaacttaactgaagtc--cttcaggaccatggcattaatgtttcatcactgtt----ccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
       |  |  | | |  | | | |   ||     |||   |||| | || ||||  ||     | | | |||| | || |    |  |  |         |   ||||||| | | |||| ||||||  ||| || ||  | ||||| || || |||||||| ||||||||| ||||||||||| | ||||| || |||||||| ||||
gtaagtttggacatgaatgcatgatgttttagcccagtatgattttgtaattgactgtcgttaatcttatggccattgtataatccgtggaaaaaaaaaaaaactattgcagCCTAGGCTGTTGGATGAGCGGCAAACAACCATATATAAAAGAGCAGTGGACAAAAATTATCACTTGAAAATGAAGTCGTCAAGGTTTATCTTCAGTGAAA

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|208386880|gb|DC956891.1|DC956891
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|67726166|gb|BJ976425.1|BJ976425
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|162241037|gb|FC416668.1|FC416668
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|162255462|gb|FC431876.1|FC431876
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|162180761|gb|FC357846.1|FC357846
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|162236928|gb|FC412879.1|FC412879
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|162236927|gb|FC412878.1|FC412878
EST:     ATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: ATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|162180762|gb|FC357847.1|FC357847
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
EST: gi|67697855|gb|BJ958088.1|BJ958088
EST:     AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAG                         CCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC
genomic: AAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGAC

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), 29 (downstream exon)
Score: 20

CCTGAGTGTATCGAACCCTGAAACGCGTGTAGATGATGCCGAGTTCGAGGAAAACGAGGTCTATGCAATTGACATCGTGACCAGTACGGGTGATGGAAAGgtattcctat ... tccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactgaagtccttcaggaccatggcattaatgtttcatcactgttccgatgcagCCCAAGTTGTTAGATGAGAAGCAGACCACAGTGTATAAGAGGGCTGTGGACAAGAATTATCACCTGAAAATGAAGGCATCAAGATTCATCTTCAGCGAAA
                         cattaat  putative branch site (score: 20)
                                         ctgttcc  putative PPT
                          attaatgttt  TA-rich tract