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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG

Basic information

species Physcomitrella patens
transcript PP1S189_118V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 7
gtaaatccaactcacgttacacgcttggtgcaccatca-cgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                    |||  || |  | ||  |   | ||       | ||  | | |    |  |||| |  | || |    | |  ||| |  ||| ||    || |    |||||| || || |||||||||||||| |||||||| || || || || ||||||||||| || |||||||||||| |||
------------------gtacgtctgttctatcacaaatacactacatttatcctatatttt----cttaatc-tagtgcaaagttcacttacttga-attgatttacttcat---cagGAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 7
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctg-aactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                    |   ||| |   |   ||    |  |  | || ||   | | | ||| |  ||||||| |   |   ||     || |  |   || || | |     |||||| || ||||| ||||| ||||| |||||||| || ||||| || ||||| ||||| || |||||||||||| |||
------------------gtaaatttgttcatctgacaattgcaatatatttgctttgattttcataaattatcattcaagttatcttacggttttgatttgattttttctatc----agGAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 7
gtaaatccaactcacgttacacgcttggtgc-accatcacgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                 ||     ||||    ||||||    |   |  |  | |   |   | ||        ||  | |   |   ||  ||| ||| |       ||| | |   ||||||  | || || ||||| ||||| ||||||||||| || ||| | |||||||| || ||||||||||||||  | |
-----------------taggaatttggaatgaccatcgactttaatata--taccatatcattatctcttggaatgttgctttatcaatagcctaaacataaaaatatgtat-gaacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 8
gtaaatccaac--tcacgttacacgcttggtgcacca-tcacgctctgtg-cagtttctgaactctgatacacaatcattctacacaaaatattacctta--acgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
||| || |     |  | ||     |||| |  | |  | |   |  |   |  |||||| |   |  || |||    |  ||   || || |   || |  || |   |   ||        ||||||  | || |||||||| ||||| || || || ||||||||  | |||||||| |||||||||||||||||  |||
gtagattccttcatttcattctcaacttgctaaagcgcttataataaggaactatttctgtatctttttataca----tattaataaagatgtagactgaggacttaaatatatgataatatcagGAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 7
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactct--gatacacaatcattctacacaaaatattaccttaacg-ttgcttct-tgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                       |||  ||||   | |   | | || ||      |  | |   |||||  ||   | || |   | |||   || | |  ||| || | | ||||    ||||||  | || |||||||| ||||| || ||||| ||||| ||| | |||||||| || ||||||||||||||  | |
-----------------------cttaatgcaaggttaacttttttgaagcaaagaattttttcaatacaatatttatgtagatgtattatggtctaagcacttgattatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 7
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgata-cacaat-cattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                |||    |||  ||||   |     | | |  |      ||| | |  ||  |||||  ||| |   | ||| | |   |||       |   | ||||    ||||||  | || |||||||| ||||| || ||||| ||||| ||| | |||||||| || ||||||||||||||  | |
--------------tattagctccttaatgcaaggttgacttttttttaagcaaagaatttttttaatacaatgtattatggtctaaacacttgatta-------tatatatctttaacagGAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
        || |||  ||| | |  |  |      | |   |||   |||||| | || |          || |    |||||||||   |  ||   | ||   | |    | |  ||| || |||||||| ||||| || ||||| |||||||| ||||||||||||||||| ||||||||||| |||||  |||
------gtaagtca--ttatatgactattat-ttgtaataatct---cagtttatcaattt---------atgaactaacacaaaatg--aatttgctggtggcacat----tata-agGTGTTAGAAGCTGTTATGATGAAGGAAAACGTGTTGCCGAGACTCTTATGTTTGATTACCATAGGCAACATGGGATTG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                             | |  |  |  | ||   ||| || | || ||| | ||  |         ||    | |||    |||| ||| ||  | |  ||  |||| || || ||||| ||||| || || |||||||||||||||||  | |||||||||||||| ||||| |||||  |||
-----------------------------gtaggagtaaacacttatcagctttt-aattctca-acttatctgcgtgtcaattcacattcttataac-ttggtttctattatg-atagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgatacacaatcattcta-cacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                    |    || | | |          | |  | ||   ||  | |  |    ||| ||   |    |  |   |  || ||  | |  ||   |    |  ||| ||  | ||||||||||| ||||| |||||||| ||||||||| | |||||||| || |||||||| |||||  | |
--------------------aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaattatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

upper sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 3'ss of exon 7
gtaaatccaactcacgttacacgcttggtgcaccatcacgctctgtgcagtttctgaactctgatacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
        | |  || | |||   |||| |         |||||||  | ||| || |     | | ||  |   ||||   |  ||  ||  |   | || | |  | | |  |  |||||| || || |||||||| ||||||||||| || ||||| ||||| |||||||| || || |||||||||||  | |
-------tagcagac-tgacatttttggcg---------gctctgttaattttatgtaggaaaaaagaccttttctctaactatgattctatat--gccttccgttatatatattacagGAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAG

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|208390897|gb|DC945914.1|DC945914
EST:     TCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTG                         GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT
genomic: TCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTGgtaaatccaa ... tcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT
EST: gi|208360291|gb|DC943021.1|DC943021
EST:     TTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTG                         GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT
genomic: TTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTGgtaaatccaa ... tcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT
EST: gi|37843082|gb|BJ601090.1|BJ601090
EST:     TTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTG                         GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT
genomic: TTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTGgtaaatccaa ... tcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT
EST: gi|208385977|gb|DC956493.1|DC956493
EST:     TTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTG                         GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT
genomic: TTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTGgtaaatccaa ... tcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGT

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: 32 (upstream exon), 33 (downstream exon)
Score: 8

GATTCTTCTCACGTCTACCTCTGAAGTTTATGGAGATCCTTTGGAGCATCCTCAGACAGAGGAATACTGGGGAAACGTAAACCCAATTGgtaaatccaa ... tcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacacaatcattctacacaaaatattaccttaacgttgcttcttgtcttgtgtagGAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTG
                           ccttaac  putative branch site (score: 8)
                                   ttgcttcttgtctt  CT-rich tract
                  aaaatattaccttaa  TA-rich tract