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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC

Basic information

species Physcomitrella patens
transcript PP1S96_93V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os02g57390.1 (Oryza sativa), 3'ss of exon 9
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                                                       ||    |  |  | |  | ||||  | | | |  || |  |||  |||  ||  | ||   ||    |     | ||   |||  | |    |   | | || | |||||||||||||| ||||||||||| || ||||| || |||||||| ||||| || ||||||||     | || ||  || | |||   || ||    || |
-----------------------------------------------------------------------ttggaataagatattgcttttctaaaat-gataccgttgctgtg-gtggatatcatgg---ctcacattcctctaaa---atgattaaagcaaatgtttcttctccagGCAATGATGAAAGACCAGTTTGCTAACTACGTGGTGCAGAAGGTTTTGGAGACTTGTGATGACCAGAACCGTGAATTGATCCTTTCACGTATCAAAGTAC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G123537_T02 (Zea mays), 3'ss of exon 8
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                           |||  |  |||      |   |||  | || | || |     ||   |   |   ||| |   |||||  |      | ||||  ||      ||  ||  |     ||  | | ||   |  || |||  | |||||||||||||| |||||||| ||||| || ||||| ||||||||  |||| || ||||||||     | || ||  || | |||  ||| ||    || |
-------------------------------------------gtttgttttca--acattcagtctcatcttgcctttttcttttagaatcggtagttcgat---ggtctgctgc---tgcaggattggactcgatgc-attctagcaacacttgtaatgtaaacttatgtcctccagGCAATGATGAAAGACCAGTTCGCAAACTATGTTGTGCAGAAGGTTCTGGAGACATGTGATGACCAGAACCGTGAATTGATTCTTTCCCGTATCAAGGTCC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA11G14550.1 (Glycine max), 3'ss of exon 10
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgtt-gtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgt-tatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                                                           ||  ||| |   |||| | ||   |   |  | |      ||    |||  ||  | |||||  |  |    ||   |||    |||| |     | | ||||||||| |||||||| || || ||||||||||||||||| || |||||  ||||||| ||||||||    ||||| |||||| | |||  |||||||   || |
---------------------------------------------------------------------------gtcagtgtggcgaatgct-ttagttaactcccagaaccacaacc-tgtaa-aatagatcttggcttgtcacaaa---atgataaatcagattccttttatatgcagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA11G14500.1 (Glycine max), 3'ss of exon 9
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgtt-gtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgt-tatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                                                           ||  ||| |   |||| | ||   |   |  | |      ||    |||  ||  | |||||  |  |    ||   |||    |||| |     | | ||||||||| |||||||| || || ||||||||||||||||| || |||||  ||||||| ||||||||    ||||| |||||| | |||  |||||||   || |
---------------------------------------------------------------------------gtcagtgtggcgaatgct-ttagttaactcccagaaccacaacc-tgtaa-aatagatcttggtttgtcacaaa---atgataaatcagattccttttatatgcagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA11G14530.1 (Glycine max), 3'ss of exon 8
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                         ||     ||   || || |||| | |   | |  |||    |||  |  | ||||   |     | || ||| ||                        ||| ||||| ||  | |         ||||  ||| |||||||||||||| || || ||||||||||| ||||| || |||||  ||||||| ||||||||    ||||| |||||| | ||   | |||||   || |
----------------------------------------acaacctgtaaa-atagatcttggtttgtcact-tgttcaaagaggcacttccttcttcc----ccagttttgcaaa-----------------------atgatgaat-cagattt---------ttcttatatacagGCAATGATGAAAGATCAATTTGCAAATTATGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGTGAGCTGATTCTGTACAGAATTAAGGTTC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA12G06450.1 (Glycine max), 3'ss of exon 8
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                          |  ||  |   || || |||| | | | | |  |||    |||    | | ||| |||     | || |    |                        ||| | |||      | |||      | ||  ||| ||||| |||||||| || || ||||||||||||||||| || |||||  ||||||| ||||||||    || || |||||| | |||  |||||||   || |
---------------------------------------acaacctgtaaaaaatagatcttggtttgccact-tgtttaaagag----gcttttccctcctccccagtttctcgaa-----------------------atgataaat------cagat------tccttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAGCGCGAGCTGATTCTTTCCCGAATTAAGGTTC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA12G06430.1 (Glycine max), 3'ss of exon 7
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                         |      ||   || || |||| | | | | |  |||    ||||      |||| |||     | || ||| ||                        ||| | ||| ||  |            | |  ||| ||||| |||||||| || || ||||||||||||||||| || |||||  ||||||| ||||||||    ||||| |||||| | |||  |||||||   || |
----------------------------------------acgacctgtaaa-atagatcttggtttgccact-tgttcaaagagt----cccttccctcttccccagttttgcaaa-----------------------atgataaat-cagattc---------cttttatatacagGCGATGATGAAAGATCAATTTGCAAATTACGTTGTACAAAAGGTGCTGGAAACTTGTGATGATCAACAACGCGAGCTGATTCTTTACCGAATTAAGGTTC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EDO96479 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                                       |        ||| |  |  |    |    | |  |  |    | |||    || | || || | |   |      | ||           |  | |   || |  || |||  | |   ||||||| |||||||||||||||||||  || ||||| || ||||||||  ||||    ||    ||    || || ||| || |||| |  |            
------------------------------------------------------cgcccaccattctgccttccccgccttct-gcaccgcgcactgcgcggcactggccctgcaactcccccgcgctccgcctc---------cgcctcctcctccg-ccacagGACCCG--GTGCAGGCCATGATGAAGGACCAGTTTGGCAACTACGTGGTGCAGAAGGTGCTGGAGGTGTGCAGCGACGAGCAGCGCGAGGTGATGCTGGCGC------------

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ35801 (Selaginella moellendorffii), 3'ss of exon 5
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcata---ggttctgtt--atgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                                                                                                        |||   ||  |    |   ||  | |  |     | || |||     || ||   |  | |||||| ||||||||||||||||||||||| ||||| || || ||||| ||||| || ||   |||    ||||| ||| |||| || || || ||    || |
------------------------------------------------------------------------------------------------------------------------gtaaagagatgaacagcaagagagagtttttcgttttgctcacgctcggctccactccacgcagGCGATGATGAAGGACCAGTTTGCAAACTACGTGGTGCAAAAGGTTTTGGAGACTTGCAGTGACCAGCAACGAGAGATGCTCCTGGGTCGTATCAAAGTCC

upper sequence: PP1S96_93V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ36402 (Selaginella moellendorffii), 3'ss of exon 6
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                                                                                                           ||   | |  ||   || ||  |    | | |   | |     || |   |     |         | |||||| ||||||||||||||||||||||| ||||| || || ||||| ||||| || ||   |||    ||||| ||| |||| || || || ||    || |
-----------------------------------------------------------------------------------------------------------gtaaag-agatgaacagcaaaagagagtttttttcgttttgctcacgctcggctcca-----ctccacgcagGCGATGATGAAGGACCAGTTTGCAAACTACGTGGTGCAAAAGGTTTTGGAGACTTGCAGTGACCAGCAACGAGAGATGCTCCTGGGTCGTATCAAAGTCC

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: 33 (upstream exon), 33 (downstream exon)
Score: 12

AAATGTGGTGGAAAAGTGCTTGGAGTATGGTGGCCCAGCTGAGCGGCAGATATTGGTCGATGAAATGCTCGGCCACACTGATGAGAATGAGCCTCTACAGgtaaggcatg ... tgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC
                             gtctgat  putative branch site (score: 12)
                                          ttctgtt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggcatggggttgataaataagatttcggacctcgcttcagttgatagtcatggagcttgatctactattacgttgtgggagtaatgttcttcactcggtttcggtcttgtaagtgcgtaggaaggggtcttgtgtgatggtgaatgcatgtctgatcataggttctgttatgcagGCAATGATGAAGGACCAGTTTGCAAATTACGTTGTTCAGAAGGTCTTGGAAACCTGTGATGAATCTCAACGGGAGCTGCTGCTTGGCCGAATTCGTGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT