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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG

Basic information

species Physcomitrella patens
transcript PP1S39_64V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os01g17010.1 (Oryza sativa), 3'ss of exon 4
ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
 |  | || |      |||       |     |  | |  |||| | | |      ||  || ||  | || | |||  |       |  | ||||||||| ||||| || || |||||||| ||||||||||||||||| ||||||||||| || || ||||| || || || || ||||| || |||||||| |||||
gtattattccctcctggttctgctattatggcatataatattctgtgagaaccaatttatgtacatgtgat-atatgctaattaatcttttgttgttcagGTGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGTGTTGGCATCAGTGGTCAAGAAGGACGGCAGGCTGTAATGGCATCAGATTTTGCGATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g21680.3 (Oryza sativa), 3'ss of exon 5
----ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
        | || |     | ||||   |  |  |    |||   | |   |||   |  || |   |  ||| ||   ||  ||| |  |  || |||  |||||||||| || || ||||||||||| ||||| |||||||| ||||| ||  | || || ||||| || |||||||| ||||| || |||||||| |||||
ccagcattttttccctactatttgaccttaattgattactcaccatgttcaacaaa-gaattgacacccttttgttttgtga-acatgtttcacttttg--cagGGGCAAATGATGTTTCAATGATACAGATGGCAGATGTTGGTGTTGGAATATGTGGTCAAGAAGGTCGTCAAGCAGTGATGGCATCAGATTTTGCCATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g20949.1 (Oryza sativa), 3'ss of exon 4
ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
       |||   |   ||    |||  ||||  ||||||     |||| ||    |||| |  | |||  |  || | | |||   | |  ||   |||| ||||| || || || ||||| |||||||||||||||||  |||||||||| || || |||||  | ||||| |||||||| || ||            
------gtacagttttttttt--ctcgccaaatattcaggaa---ttacttga---tttactatatttttctcaatctgaaaagagGTACCTTT--CCAGGTGCAAATGATGTATCCATGATTCAAATGGCTGATGTTGGTATTGGCATCAGTGGACAAGAAGGAAGGCAAGCTGTTATGGCATCAGA------------

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM5G840699_T01 (Zea mays), 3'ss of exon 4
ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcacttta---ttacatgtcacaaggcttgc--tattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
   || ||| |       ||   ||||| |  |       || | ||   | ||   ||  |    |  |   | | || | |     ||| |  |   ||||||| ||||| || || |||||||| |||||||||||||||||  |||||||||| || || ||||| |||||||| |||||||| || |||||| | |||||
---gtattattccctc-ctgcttctctt-attatggtgtattttattctctatgatcttgatatgttcaaatctgatatatgaatttccttaccttggcgttcagGCGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGGATTGGCATCAGTGGCCAAGAAGGTCGACAAGCTGTTATGGCATCAGATTTTTCTATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G398288_T01 (Zea mays), 3'ss of exon 4
ttcgtgttactagtaagttgaagctcttcaaaacttcaggttct---cttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgtt-cagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
| | | ||| |  |  |   || ||    |  |  |||   | |    || || ||  |   |   ||    | | |   | ||   | ||  | || |  |||||||||| || || ||||||||||| |||||||||||||| ||||||||  | || || ||||| || || ||||| ||||| || || ||||| |||||
tccatcttattcttggg---aatcttcatattatgtcacactttaagtttccaagtaacgcgaagacaacagagt-ctcattaccctgtttaatcttttggcagGGGCAAATGATGTTTCAATGATACAGATGGCTGATGTTGGTGTTGGCATATGTGGTCAAGAAGGTCGTCAGGCAGTGATGGCTTCAGACTTTGCTATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G407825_T01 (Zea mays), 3'ss of exon 4
-ttcgtgttactagtaagttgaagctcttcaaa-acttcaggttctcttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
 ||  |   |||   ||  |    |     ||  |  ||||    || || |||| |  |     |   | |  | || | | ||  | | |   | |||||| ||||| || || || ||||| ||||||||||| |||||  | |||||||| ||||| || ||  | ||||| |||||||| || |||||||| |||||
attattccaacttaaaatgtaggacaaaggaagtagctcagaacttcatatatgttttatcttcacgagtcaaaaaatatgaaaa--catacacgttttcagGTGCAAATGATGTATCCATGATTCAAATGGCTGACGTTGGCATCGGCATCAGTGGGCAAGAGGGAAGGCAAGCTGTTATGGCCTCAGATTTTGCCATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
---------------------------------ttcgtg---ttactagtaagttgaagctcttcaaaacttcaggttc-tcttacatgtgtctttag-tgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
                                 |||      ||  ||| ||    ||    |   ||  ||  || |  ||| |  | |||  | || || | |  ||| |||    || |   || ||   | |||| || || || || |||||||| ||||||||||||||||||||||||||||| || || ||||| || ||||| || ||||| |||||||||||||||||
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatg---tgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
-------------------------------ttcgtgttactagta--agttgaagctcttca--aaacttcaggttctcttacatgtgt-ctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
                               |||       |  ||  | | |||  | || |  |   ||  | |  ||| |  | ||| || | ||| | |  ||| |||    || |   || ||   | |||| || || || || |||||||| ||||||||||||||||||||||||||||| || || || || || ||||| || ||||| |||||||||||||||||
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatg---tgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G44550.1 (Glycine max), 3'ss of exon 7
--------------------------------------------------------------ttcgtg-ttactagtaagttg-aagctcttcaaaacttcag---gttctcttacatgtgtctt--tagtgcactttattacatgtcacaaggcttgctattgtt--------------cagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
                                                              ||  || ||  |||||| ||| | |    || |  ||||||   ||  |   | |||  | ||  |     | || |||  || | |      |   | |||||              ||||||| || |||||||||||||| |||||||| |||||||| || || ||  | |||||||||||||| |||||||| ||||| || |||||||| |||||
gtaagttatttataatatgaaattgcacttaatttgcatttgggtgttgttgtgaggcctggttgatggttgatagtaatttgtatggcagtccaggcttcagctagtgtttccagatggattttgatgtaagatttgatttaatatgaacttaatcttttttgttttgattacttttgacagGGGCCAATGACGTGTCAATGATCCAAATGGCAGATGTTGGTGTAGGGATATGTGGGCAGGAAGGGCGCCAAGCAGTGATGGCATCAGATTTTGCTATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA16G34610.1 (Glycine max), 3'ss of exon 4
-------ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
       || ||  |     |||   || || |||  ||| || || || |     ||    |||   ||   | |  |   |||  |||   || || |||  |||||||||| || || |||||||| |||||||| |||||||| ||||| ||  | |||||||||||||| |||||||| ||||| || |||||||| |||||
cttgtagtttgttatttgtataatcagatgcacttttaaa-ttaagattattccgtatcaaactt--atgacgtcttctgtttgtttcaa---ttact-ttggacagGGGCAAATGATGTTTCAATGATCCAAATGGCAGATGTTGGTGTTGGAATATGTGGGCAGGAAGGGCGCCAAGCAGTGATGGCATCAGATTTTGCTATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA15G29860.1 (Glycine max), 3'ss of exon 6
-------------------------------------------------------------------------------ttcgtgttactagtaagttgaagctct--tcaaaacttcaggttc-tcttacatg-tgtctttagtgcactt-tattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
                                                                                       |  |  |||   | || ||  |  ||| | ||| ||  | || | || |||  ||  ||   || ||| | ||           |||| || || ||| || || ||||| |||||||| ||||||||| ||||||||||||| ||||| || ||||| || || ||||| || ||||| || ||||||||||||||
gtatgaaatcttgtatttacttgtttaggattgtcatttcccttcaaaagaataaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtggtttttgtgtttgtataaaataatctttattatgcttttctttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA09G41040.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------ttcgtgttactagtaagttg-aagctcttcaaaacttcaggttctcttac---atgtgtctt--tagtgcactttatt--acatgtcacaaggcttgctattgtt--------------cagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
                                                          |  |||  |||||| ||| | |    || |  |||||| |  | || |   |||  | ||  ||    | || |||  | |||     |  |||  | || |               ||||||| || || ||||||||||| |||||||| |||||||| || || ||  | |||||||||||||| |||||||| ||||| || |||||||| |||||
gtaagatatttgtaatatgaaattgaacttaatttgcatttgggtgttcttgtgaggcctggttgatagtaatttgcatggcagtccaggcttcagatagtgttgccagatggattttgatataagatttgatttaatatgaacttaatcttttttttatctcgattacatttgacagGGGCCAATGATGTGTCAATGATCCAAATGGCAGATGTTGGTGTAGGAATATGTGGGCAGGAAGGGCGCCAAGCAGTGATGGCATCAGATTTTGCTATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA08G24580.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------ttcgtgttactagtaagttgaagctct--tcaaaacttcaggttc-tcttacatg-tgtctttagtgcactt-tattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
                                                                                       |  |  |||   | || ||  |  ||| | ||| ||  | || | || |||  ||  ||   || ||| | ||           ||||||  || ||| || || ||||| |||||||| ||||||||| ||||||||||||| ||||| || ||||| || || ||||| || ||||| || ||||||||||| ||
gtatgaaatcttctatttacttgtttaatattgtcatcttccttcaaaagaatgaaaataaaataggataacaaagtgaacaaaagaaagaaaaagaaaaggcactggtagaaaatacagattaattttgcttggtgtgatttttgtgtttatataaaataatctttattatgctatattttagGTGCTAATGACGTATCAATGATCCAAATGGCTCATGTTGGAGTTGGAATCAGTGGACAGGAGGGTCGGCAAGCTGTAATGGCTTCAGATTTTGCAATTGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA13G18580.1 (Glycine max), 3'ss of exon 7
----------------------------------ttcgtg---ttactagtaagttgaagctcttcaaaacttcaggttc-tcttacatgtgt-ctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG--
                                  |||      ||  ||| ||    ||    |    |  ||  || |  ||| |  | ||| || | ||| | |  ||| |||    || |   || ||   | |||| || || || || |||||||| ||||||| |||||||||| ||||| |||| || || ||||| |  ||||| || ||||| |||||||||||||||||  
gtaattgattttttgttagaccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaattccattatgcatg---tgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGTTGATGTTGGAATTGGCTTCAGTGGACAAGAAGGTC--CAAGCTGTAATGGCATCTGATTTTGCAATGGGGC

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
------------ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttagtgcactttatta--catgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
             || | || | |  |||| |    ||| |   |       |   |  ||     ||||| ||    | | ||   | | ||| | |  |||   ||   |||| || || || || || ||||| ||||||||||||||||| || || || ||||| || ||||| || ||||| || ||||| |||||||| ||||||||
gtaatgaccccactcttctttccaaaaagtag----tctgcctgatcctgtctaaacagacccagttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
---------------------ttcgtgttactagtaagttgaagctcttcaaaacttcaggttc---------------tcttacatgtgtctttagtgcactttattacatgtcacaaggcttgc-tattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
                     |   |   |||  ||| ||     |   ||| ||   |   |                ||| |  |||   ||   |  |   ||   | ||  |      |||  |  |   |||| || || || || ||||||||||||||||||||||| ||| |||| ||||| || || || || || ||||| || ||||| || ||||||||||||||
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggctaacgcttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG

upper sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv08s0058g01400.t01 (Vitis vinifera), 3'ss of exon 4
ttcgtgttactagtaagttgaagctcttcaaaacttcaggttctcttacatgtgtctttag--------tgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
      || |  | |        | | ||    |||| || |  |  ||||  ||   |||        ||| ||||  | | | | || |  ||  |   ||| |||| || ||||| || |||||||| |||||||| |||||||| || || ||  | || ||||| ||||| |||||||| ||||| || ||||||||||||||
-----cttgcctgcacaccaccccccctcccctcttctgggta-cacacattggttgctaggctggtattgctctttccttcctcttacta--ctgacacctgtgcagGTGCCAACGATGTTTCAATGATTCAAATGGCAGATGTTGGTGTGGGAATATGTGGTCAGGAGGGGCGTCAAGCAGTAATGGCATCGGATTTTGCAATGGG

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|34832448|gb|AJ566713.1|AJ566713
EST:     CTCTCTTGTGAAACGCAAAAGCAAAGATATGACGTTGGCCATTGGTGATG                         GGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCA
genomic: CTCTCTTGTGAAACGCAAAAGCAAAGATATGACGTTGGCCATTGGTGATGgtaagttggc ... tattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCA




















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), 21 (downstream exon)
Score: 4

AAGGTTGTCGTATGTTGTCGAGTTGCACCTCTTCAGAAAGCGGGTATTGTCTCTCTTGTGAAACGCAAAAGCAAAGATATGACGTTGGCCATTGGTGATGgtaagttggc ... tattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacatgtgtctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
 ctcttac  putative branch site (score: 4)
                     tttattacat  TA-rich tract