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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG

Basic information

species Physcomitrella patens
transcript PP1S425_2V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os02g13110.2 (Oryza sativa), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
         || | |    | |  | |||    || |  | | |   |||||        |   | |  | |  |     ||| || | | |||| ||||||||||||||| ||||| || |||||||| || || || ||||| |||||| | ||||| |||||  | ||||| |||||||| || |||||
------gtgaagttt---cgtaacctgaatgatggcaaaaat-gtcaatgttaagacatgtcacaatctaatgccgtg--ttaatttcatctttt-gcagCTCTGTGATCTATATGAAAATGATTCAATATTTGACAAATTTGAATGTTGTCTGAGTGGGGATGGACTTCGTGTTGCAACTGGCTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttt--tttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                      |  |||    |  ||     ||  ||       | | | || ||       ||| ||  ||  |    | |  ||| ||| | |||||||| ||||||||||| ||||| || || || |||||||||||| | ||||| |||||  | | ||| ||||||||||| ||  |
----------------------gtgagactttgtcaaccgaatgactaaaaagaagccatatg-atgactgatacataatctagctgtactctaattttcagTTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G165418_T01 (Zea mays), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgt--ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                  ||||       ||   |||| | ||    | |    | |    || |   || | |   || ||  | |  |   |  || |||||||||||||| || ||||| || ||||| ||||| ||||||||||| ||| | ||||| |||||  | ||||| ||||||||||| ||  |
-----------------gtgaaattctctcaactgaat-aattaaaaaggaagctatttgatgaacaaaagtaatgtaattttatgatatcactactttcagCTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA15G02640.1 (Glycine max), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgc-agCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                  |||     ||   |    || | ||  ||     ||| | || ||  ||  |       |   |  ||   |     ||| |||| |||||| | ||||| || |||||||||||||||||||| || |||||| | ||||| |||||  |||| |||||||||||||| |||||
---------------gtttgataagtgat--gaattatgaatttctttctactgttttgtctgagttataactggttatgctttttgtttgaacgtgccagCTTTGTGATTTATATGAAAATGATTCAATCTTCGATAAGTTCGAATGTTGTCTAAGTGGTGATGGATTGCGCGTAGCAACTGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaatta-cttacgtttttttg--cagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
            || |     | |   |     | ||| ||     |   ||  ||  | || |||  |  ||| || || |  || |  ||||||||  ||||| |||||| | ||||| || |||||||| || |||||||||||||||||| | ||||| |||||  |||||||  |||||||||| |||||
----------gttagattcccatgtttatataagtaatgagcaa--tgaattcctgctgctt-tatcaag-tcatagtaactggctcatttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttg-gttatg--tttgtgtcgtttgtattgaactcacagaaattacttacgtttttttg--cagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                      |  |||         || | || |  |||  ||| ||  | || |||  |  |     || |  ||    ||||||||  ||||| |||||| | ||||| || |||||||| || |||||||||||||||||| | ||||| |||||  |||||||  ||||||| || |||||
----------------------gttagattcccatgtttggatgagcaatgaatttctgctgctt-tatcaagttatagtaactggctcttttttttttggccagCTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaat-tagttggttatgtttgtgtcgtttgtattgaa--ctcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                      |  ||| |       | | |    || | |||||    | ||| |||||  || ||     |   ||        |||||||| || ||||| ||||| || || || ||||| ||||| |||||||||||| | |||||||||||  || | |||||||| ||||| |||||
----------------------gtgagagcttctttctgtggcatcttttatttgttgattctgtgttgaaagctaaccacgttatgttttacccggttgcagCTATGCGATCTATATGAAAATGACTCCATCTTTGATAAATTTGAGTGTTGTCTGAGTGGCGATGGATTGAGGGTAGCAACAGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 12
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattac--ttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                   |   |      |      | ||   | ||  ||||    ||| ||  |   || |  |  ||| |  ||  | |  ||| |||||||||||| | ||||| || ||||| ||||| || ||||| ||||||||| | |||||| ||||| |||| | ||| || ||||| |||||
-------------------gtcagtttcctaatattttgagagagatacatttggcgagttggtgctttgctgaatggtattccctttgtggtcattttcagCTCTGTGATTTATATGAAAATGATTCCATCTTTGACAAGTTCGAGTGTTGTATAAGTGGCAATGGCTTGCGAGCAGCTACAGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
  | |       |    | |||            |||  | ||   ||  ||  | || |   |  | |  | ||      |   |    || | | ||| | |||||| | ||||| || ||||||||||| ||||| ||||| |||||| | ||||| ||||| ||||||||||| || ||||| |||||
-gtgagcttgctttcctcagaaaagtcttacacagaacaactt--ctacattactctc-tgcatgctaattttaccctctgtttctttccttctctccagTTGTGTGATTTATATGAAAATGATTCAATCTTTGATAAATTTGAATGTTGTCTGAGTGGTGATGGAATGCGTGTAGCTACAGGTTCTTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 10
----------cttcaatcaaaatata---actgaaggcagaacaggggaattagttggtta---tgtttgtgtcgtttg---tattgaactcacagaaattac-ttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
          ||||  |  |||| ||    || |||||  || | |  |  ||  |  ||    |   ||| || |||     ||     |    | | ||    |  | | ||   ||| | || ||| | ||||| || ||||||||||| || ||||||||||||||| | ||||| ||||| |  || || ||||||||||| |||||
gtgcgattttcttcttttgaaatctatcatctaaaggccaaataagcaacctatataattgatctaagtgtatcattttatccataatgatggtgggacttgtactctgatcttgatcagTTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------cttcaatcaaaatataactgaaggcagaacaggggaattagttgg---ttatgtttgtgtcgtttgtattg--aactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                        | |  |     |    ||       |||  | |  |||  ||||   ||||  |    |  | || | |    | | |     |||| |||  | ||  | ||||| |||||| | ||||| || ||||| |||||||| || |||||||||||| | ||||| |||||  | || || || ||||||||||||||
gtgatttcacttcttcatgaagcttcctttttttttggtgctttgatttgaatggagttatt--ttgggctttattgtcaaataatatgaactatttaattattatcattatttaaatcttgat-cagCTGTGTGATTTATATGAAAATGATTCTATCTTCGACAAATTTGAGTGTTGTCTGAGTGGAGATGGACTACGAGTGGCGACTGGTTCCTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgttttt---ttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                                        ||||  | | |   ||||||| |  | |   |||| ||  || ||     ||||   |||||| | |||||  | ||||||||||||||  | ||||| || || ||||| ||||| |||||||||||| | ||||||||||| || ||||||||
----------------------------------------gttgcgtctttcgatgtcgttcgggtgg---tcactgactttgctggttcttttgcgttgcagTTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAG

upper sequence: PP1S425_2V6.3 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 10
cttcaatcaaaatataactgaaggcagaacaggggaattagttggttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                                        ||||  | | |   ||||||| |  | |  |             ||   ||   |||||| | |||||  | ||||||||||||||  | ||||| || || ||||| ||||| |||||||||||| | ||||||||||| || ||||||||
----------------------------------------gttgcgtctttcgatgtcgttcgggtggtccctgactttgcgggttcttttgcgttgcagTTATGTGACTTGTATGAGAACGATTCTTTATTCGACAAATTCGAGTGCTGTTTAAGTGGCGATGGCCTCCGTGTAGCAACCGGATCCTACAG

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|37835757|gb|BJ593769.1|BJ593769
EST:     AAAGTTCACGAGCATTTGCGACCAAAG                         CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT
genomic: AAAGTTCACGAGCATTTGCGACCAAAGgtgaaccttg ... ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGT




















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: 29 (upstream exon), 35 (downstream exon)
Score: 7

CTGTGGGATGTGAACATGGAATCTGCTCCTGTGGCTACATTTAAAGTTCACGAGCATTTGCGACCAAAGgtgaaccttg ... ttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgtttgtgtcgtttgtattgaactcacagaaattacttacgtttttttgcagCTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAG
                                    tacttac  putative branch site (score: 7)
                                          cgttttttt  CT-rich tract
                                aaattactta  TA-rich tract