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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG

Basic information

species Physcomitrella patens
transcript PP1S99_260V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 12
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                    |||  |||  || |||    |||  | |  | ||    || | |  || |      ||    | | | |   |  ||  | |  |     |||  |  |||| ||||| ||  | |  ||    ||||| | ||| ||||||||||||||||| || || |||||||||||||||||  | ||||| |  ||||||
--------------------------------------------------------------------gtgagtttctgtgatt---gcatgagttctgggactgaaagtctctttgt------ttaacccagaagtgctaagttttatgggcac---catattctagGTCTGGGAGGCCACTAGTGGAGCAAAGCAATTTACATTTGAAGGTCATGAAGCTCCTGTTTACTCTGTTTGTCCACATTATAAGGAAAATATTCAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 13
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacata--tggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                             | |  ||   |||||  | || | ||| | ||| | | | | || ||||          ||    | ||     |   ||  | ||  | ||||| |||||||| |  || ||    ||||||||||||||||| |||||||||||||| || || ||||| || || || ||||| || || ||||||
-----------------------------------------------------------------------------gttagttgtcacataatttgtcatagatatcaa-tatcaatataaataa--------aaaaaccaatttcaagtg---ttcaagattttgcagGTATGGGATGCCGTTACTGGTGCAAAGCAGTATACTTTTGAGGGTCATGAAGCACCTGTATATTCTGTATGCCCTCATCACAAAGAAAGTATTCAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA17G12110.1 (Glycine max), 3'ss of exon 13
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                             | |  ||   ||||||  ||  | |||     | | | | |  ||||    |     ||    | |||  | |   ||  |  || | ||||| |||||||| |  || ||    ||||||||||||||||| |||||||||||||| || || ||||| || || || ||||| || || ||||||
-----------------------------------------------------------------------------gttagttgtcacatattttgttataga-----tatcaatatcaataaaaaaa-----aaaacaattttaaatg---ttcaaggtcttgcagGTATGGGATGCAGTTACTGGTGCAAAGCAGTATACTTTTGAGGGTCATGAAGCACCTGTATATTCTGTATGCCCTCATCACAAAGAAAGTATTCAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA15G00880.1 (Glycine max), 3'ss of exon 12
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                                          || | |     |  |   |  ||    |   ||| || |  |   || || |  |  || || || | || | || |||||||||||||||| || ||   ||| ||||||||||| |||||||||||||| || || || ||||| ||||| ||  | || || | |||||||
-----------------------------------------------------------------------------------------gtaggtttgccaaagcatgagcttggatttcttaagtgaagataacatatgtcacta-actaagttatgcaac-ttaagGTTTGGGATGCTGCTACGGGTGCGAAACAGTATACTTTCGAAGGTCATGAAGCTCCAGTTTATTCTGTCTGTCCGCATTATAAAGAAAACATTCAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA08G22910.2 (Glycine max), 3'ss of exon 13
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttatt--ctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                                          || | |   |||     |  ||  ||  ||  |     | | ||| ||| ||    |  || || || | ||   || |||| |||||||||||  | ||    |||||||||||||||||||||||||| || || || || ||||| || |||||  | || || | |||||||
-----------------------------------------------------------------------------------------gtaagttttcagaacatgagcttggtttgctgaagtggaggaactg-aatatgttgcta-actaaattatgcaat-ttaagGTATGGGATGCTGCTTCGGGTGCAAAGCAGTATACTTTTGAAGGTCATGAGGCTCCTGTTTATTCTGTCTGCCCACATTATAAAGAAAACATTCAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                         ||||  ||  |||  ||               | |||||   |  | ||  |    ||||||     | | |  || || ||  |  | || ||||| ||||||||    || ||    ||||||||||||||||| |||||||| ||||| || || ||||| |||||||| |||||||| |  ||||||
------------------------------------------------------------------------gtttgttttgcttcctca---------------ctaatttcggtgga-atggtaaggtctggatgccaattat--acaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 12
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgt-acatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                              || |     |  | |  |||| |        ||  ||| || ||  || | | |    ||| || ||     |       | ||    ||||| ||||||      |  ||| |||| |  | || ||||||||||||||| || || || || ||| | ||||| || ||||||||||||||||||
------------------------------------------------------------------------------gtgaaagggagttttcatgagtgttttttgtttaaattgtaaatccttcttttttcctttttacgttctctaagtgaaagaaatgaaacagGTCTGGGATAT---GAACGGGAGGAAACTATTTAATTTTGAAGGTCATGAGGCTCCAGTATATTCTATATGTCCCCATCACAAGGAGAGCATTCAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 12
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                                                                   |||  |||||  |      || |      || | |  |   |  |    |||||| |||||||| |  |  || || ||  | || |||||||| ||||| ||||| || ||||||||||||||||| || |||||||| |  || |||
------------------------------------------------------------------------------------------------------------------gtctgcataatctttgagaaaaatatggactgaaagggca-atgaaaaaatcagGTGTGGGATGCGGTGAGTGGTCGCAACAAATACACTTTTGAGGGTCACGAAGCGCCAGTGTACTCTGTTTGTCCGCATCACAAGGAAAATATACAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 15
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                ||  |    | ||  | ||||||   | ||| ||     |    ||     |||  |||||  |      || |      || | |  |   |  |     ||||| |||||||| |  |  || || ||  | || |||||||| ||||| ||||| || ||||||||||||||||| || |||||||| || || |||
----------------------------------------------------------------gcaagcaactgtgcataatttct---tgtggcgatgacaaaacgatcaaggtctgcataatctttgagaaaagtatggactgaaagggcg-atgaaaaaaccagGTGTGGGATGCGGTGAGTGGTCGCAACAAATACACTTTTGAGGGTCACGAAGCGCCAGTGTACTCTGTTTGTCCGCATCACAAGGAAAGTATACAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 12
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                                                                   |||  |||||      | ||  | ||||   ||   |    |  |    |||||| |||||||| |  |  || || ||  | || |||||||| ||||| ||||| || ||||||||||||||||| || |||||||| |  || |||
------------------------------------------------------------------------------------------------------------------gtctgcataatc----tttgagatggact---gaaagagcaatgaaaaaatcagGTGTGGGATGCGGTGAGTGGTCGCAACAAATACACTTTTGAGGGTCACGAAGCGCCAGTGTACTCTGTTTGTCCGCATCACAAGGAAAATATACAG

upper sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 12
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                                                                                                                   |||  ||||| ||      || |      || | |  |   |  |     ||||| |||||||| |  |  || || ||  | || |||||||| ||||| ||||| || ||||||||||||||||| || |||||||| || || |||
------------------------------------------------------------------------------------------------------------------gtctgcataatcgttgagaaaagtatggactgaaagggcg-atgaaaaaaccagGTGTGGGATGCGGTGAGTGGTCGCAACAAATACACTTTTGAGGGTCACGAAGCGCCAGTGTACTCTGTTTGTCCGCATCACAAGGAAAGTATACAG

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: 28 (upstream exon), 25 (downstream exon)
Score: 8

ATTGACGCACATGTTGGCGGTGTTAACGATCTTGCCTTTTCTCATCCTAACAAACAACTATGCGTTATCACATGCGGAGATGACAAAACTATCAAGgtgcgcactt ... catccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG
                      atttgac  putative branch site (score: 8)
                                             catccttc  putative PPT
       ataattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA