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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA

Basic information

species Physcomitrella patens
transcript PP1S167_51V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                                                                                      || ||||| || |   |    |  || | |||  |   |     | |||  |  ||         |   |     ||    |  || | |  | |    ||||||||||| | || |||||||||||||||||||||||||| || || || ||||| ||||| |||||     | |  | | |  | ||||| ||||| |
-----------------------------------------------------------------------------------atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtttttttgatgaactgttct----agTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                                                                                            ||| | |  | |||| |||  |  ||||| || |     | |||   | | ||     | || ||   || | | | || |  || |||   |||||||||||| | ||||||||||| ||||||||||| || || ||||||||||||||||| || || || |  ||||  ||  |  | || || ||||| |
-------------------------------------------------------------------------------------------gtatttgatttactctgttttcttcttactcagctatttggctataccttttat-----ctgtctt---ttcatgct-ctatccttgtttac-cagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                                                                                            || || ||   ||  |   || ||||       || | ||| ||  |  || |  ||| | |  ||  |   |  | || |      |  | |||||||| ||  | ||||||||||| ||||||||||| ||||| ||||| |||||||||||| | || || |  ||   |||  |  ||||||| || || |
-------------------------------------------------------------------------------------------gtacattaaaa-cttatcaccagatttc----acttacgagtaattgtgttcct--tgagc-tactcaataagct-tgcttttcaatctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                                                                          || || | ||    |  |  || ||   |     ||  |  |||      |||| |  || |  |||  | ||  |   | |||| |            |||||      |||||||||||  | ||||||||||||||||||||||| |||||||| |||||||||||||| || || |||   ||   |||  |  | || || |||||||
-------------------------------------------------------------------------gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttttcttactaaatctagactattcgttc-----------atttc------cagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                                                       || || | |      ||  |    | | | || |  || | |  ||  | ||||       | |||| | |   || |    ||||    |||||         | |||          | ||| |   |||||||| ||  ||||||| ||||||||||||||||| |||||||| || |||||||| ||||| || || |  || | |||  |  | ||||||||||| |
------------------------------------------------------gtatttctttcatcagttact--cctgcctgaagt--ttgtttgcaccacccttt-----gctcactaggctctgaaatg--tttta----attgatgccacattgcttat---------tctctgtgctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtt-tgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                              ||    ||| |  ||| ||          ||||| |  |  ||||  || || ||   || || ||||    ||| | || |||  |||||    | || || |||  | |     ||| |   |||| |  ||                     |||||||| ||  | ||||| |||||||| |||||||| ||||| || ||||||||||||||||| || |||  ||| | |||  |  | || || ||||| |
------------------------------gtgtcctttaagaatttcg----------tttctgggttgctgatgattaccata---tccttttatct-tgtctgtcttccatccttactggactctggaatttaattctgc---atttaatatgtttgaatt---------------------cagTTTGACTATCTCAAGAGCTTGGAAATTGAGGAGAAAATCAACAAGATTAGATGGTGTCAGACAGCTAACAGCGCACTGTTTCTTCTCTCCACTAATGATA

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 3
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttct---ttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                                                                                                                               |   | |  || |||| | |  | ||||||     |||  |||| |  || |   |||  |||||||| ||| | |||||  |||| |||||||| |||||||| ||||| ||||||||||| || || |||| |||||  ||  |  | || || |||||||
-------------------------------------------------------------------------------------------------------------------------------gtgcgcttgctctatcgt-tgaagcgtgttgatgctacattacttttgttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

upper sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
gtaatgttagcaacgctaaggtgagtcgtggtaatttttcaagattgcgcccacatagttttctagaatattgatagtttccttaaaatcattatatcaacttctctttttcatatttactaagtttgcaagttatctttatcatattgaccgtgttcggtttacgatactgtatttcttt-----ctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
                                                                                                                               |   | |  || |||| | |  | ||||||     |||  |||| | ||| |||     |  |||||||| ||| | |||||  |||| |||||||| |||||||| ||||| ||||||||||| || || |||| |||||  ||  |  | || || |||||||
-------------------------------------------------------------------------------------------------------------------------------gtgcgcttgctctatcgt-tgaagcgtgttgatgctacattactttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

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: 35 (upstream exon), 31 (downstream exon)
Score: 3

CAAAGGACACGGAGAGAGTTGGAAAGAGCTGATTCTGCGGGGTCCAGGCATCCTGAATATCGATACTCTACCGAGTTTCAAAGTCATGAACCAGAGgtaatgttag ... ctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctttatcatattgaccgtgttcggtttacgatactgtatttctttctgcagTTTGATTACTTGAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGTCAGACTGCCAACGCCGCTCAGTTCTTAATTTCTACGAATGACA
            tattgac  putative branch site (score: 3)
                                     ctgtatttctttct  putative PPT
     tttatcatatt  TA-rich tract