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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag

Basic information

species Physcomitrella patens
transcript PP1S159_105V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os05g49100.1 (Oryza sativa), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag-----
| || ||  |||  ||    | ||| || |||  | | || ||||| |     |||||||| || ||||||||||||||||||||||||||   ||| ||||   ||   | |        ||   |    || ||       |  | || | |  |||      |  |  |   ||  |  |||  |  |  | |  ||     
GGTTCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGATGGCTACCGGTGGCGCAAGTACGGCCAGAAAGCCGTCAAGAACAGCCCATTTCCCAGgtacttcgttttatattataagtc-gttttaattttttt----taattaaattttcttaagtttgatcaaatttataggaatgtttagcaacgtctatagcacca

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os07g02060.1 (Oryza sativa), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag-
| || ||  |||  |||   | |||  | ||   | |||| ||||| | |   ||| | || |||||||||||||||||||||||||| |||  ||||||||   |     ||       | | ||    |||||       ||    ||  |  |   ||   |   ||  |||     | | | | |  |   | |   
GGTTCGCGTTCATGACGAAGAGCGAGATCGATCACCTGGAGGATGGCTATCGCTGGAGAAAGTATGGCCAGAAAGCCGTCAAGAACAGTCCTTTTCCAAGgtgcctacctacattttatacatataaattcatatatggagtattacaaatgcatgcatgctgtagtaataagat-gtctttgctttaatttggtttctct

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os05g50610.1 (Oryza sativa), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagca-acaagtatctgattaaaatcgtt-ctgagatatgtgcag------
|  | ||  |||  ||    | ||| || |||  | | || || || |     |||||||| || |||||||||||||||||||||||| |  | |||||||  | || | ||         || |    ||||| |     ||  || |   || || |||  ||  ||| |||   ||   | | |      ||  |||       
GTGTGGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGACGGCTACCGGTGGCGCAAGTACGGCCAGAAAGCCGTCAAGAACAGCTCCTACCCAAGgtcag-ctagccaa-----attttcacttgcatatgcatt--attctccatcataattggcatgcatatatttgacagaagcagctaccacagcattagcaacaagct

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g47560.1 (Oryza sativa), 5'ss of exon 4
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtca-ccacgcgcgtttatcaccatattccccccatcttcaagtcta-gttagcaacaagtatctgattaaaatcgttctgagatatgtgcag-----------------------------------------------------
| || ||  |||  ||    | ||| || |||  | | || || || |     |||||||| || |||||||| |||||||||||||||||  | || ||||  || ||  ||   || | |   ||| |  |  |  | |  | ||    |  |      | | |         | |   | ||  |        | || |                                                     
GGTTCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGACGGCTACCGGTGGCGCAAGTACGGCCAGAAGGCCGTCAAGAACAGCCCATACCCCAGgtacgtatgtacagttacacacacgtat-agtacgtgactcgtagctgtgcgcgtgtacgtgtaccggccgcagtagttgcaccggacgcgcgcgcgcgcggcagaatgcgatgattgcaatgatctgatatatacggggttgatttttttgcag

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G453571_T01 (Zea mays), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag-
| || ||  |||  ||    | ||| || ||   | | || || || |     |||||||| || ||||||||||||||||||||||||||   ||| ||||   |     | | ||       ||        | |||    | |||        ||  ||  ||   |||   ||  ||     |  ||  |    || 
GGTTCGCGTTCATGACCAAGAGCGAGGTCGATCACCTCGAGGACGGCTACCGGTGGCGCAAGTACGGCCAGAAAGCCGTCAAGAACAGCCCGTTTCCGAGgtacatacatac-ctacataatgctacatatgcgtacccttttttttccctctctttttacacaaaagctctatatatgatgcacgtacgaattagctagc

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G151763_T01 (Zea mays), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttat-caccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag-
| || ||  ||   ||    | ||| || |||  | | || || || |     |||||||| || |||||||| |||||||||||||||||  | || ||||  || |    |      ||    || ||  | || |     |  |  |  |  |   |||| |   |||  | |||   |  | |||  || ||  | | 
GGTTCGCGTTCTTGACCAAGAGCGAGGTCGACCACCTTGAGGACGGCTACCGGTGGCGCAAGTACGGCCAGAAGGCCGTCAAGAACAGCCCATACCCCAGgtacgtatatgtatatattgcaggcatacattacatacatgatacatggacatgcacagagca-cgtatatacggttaccctactgctgc-atctgcactgc

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM5G812272_T02 (Zea mays), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgt---ttgtctggtcaccacgcgcgtttatcaccatattc-cccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatg-tgcag--------------------------------------
|  | ||  |||  ||    | ||| || |||  | | || || || |     |||||||| || |||||||| |||||||||||||||||  | || ||||   | ||     |||  | ||  | ||   | |||    |   |  || || || ||   |||| |   | |  |||   | ||    |||  || | | | |                                      
GGATCGCGTTCATGACCAAGAGCGAGGTCGACCACCTCGAGGACGGCTACCGGTGGCGCAAGTACGGCCAGAAGGCCGTCAAGAACAGCCCATACCCCAGgtacgtggtacatgcacagcacgtatatacagctatacctactggctactgcacgtatatacagcacctc-tcttcgatcctactc--catgacgtacggtacggtagacattgctgcatgagctaatggtgatggcgtgcag

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G143204_T02 (Zea mays), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaaca--agtatct--gattaaaatcgttctgagatatgtgcag
| || ||  |||  ||    |||||  | ||   | | ||||| || | || |||| | || |||||||||||||| |||||||||||||||   |||||||| ||     ||   |     |  ||   |     |     | || | |  |||||    |||   | || ||  |  |   || ||       ||||| || 
GGTTCGCGTTCATGACCAAGACCGAGCTCGATCACCTCGACGACGGCTATAGATGGAGGAAGTATGGCCAGAAAGCTGTCAAGAACAGCCCTTTCCCAAGgttggttc---cattgcttaaatagatggacgggacctaataaactgctaagctagtgtaaaaccttattagctatgtcttgcattgtctaattttatgtaca-

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AC198725.4_FGT009 (Zea mays), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcg-cgtttatca-ccatattccccccatcttcaagtctagttagcaacaagtatctgat-taaaatcgttctgagatatgtgcag
|  ||||| ||   ||    | ||| |||||   | | || || || | |   ||||||||||| |||||||| || ||||||||||| ||| | ||||||| ||| |    ||    |  ||||   || |  | |||     |  | || |  |  |  ||   |  ||||  |  | ||  | | | |  |  |  || |
GCGTTGCCTTCCTCACCAAGAGCGAGGTGGATCACCTTGAGGACGGCTATCGGTGGCGCAAATACGGCCAGAAGGCGGTCAAGAACAGTCCTTACCCAAGgtctgtatatatacttttcttcgttccccatctttgttcattataattgcatgcatgatatgc--tagctatcacacatgaaggcatgcagctaccta-gctg

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA17G03950.2 (Glycine max), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtt-tatcaccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgt-gcag--------------------------------------------------------------------------------
|||||||  |||  ||    |  || |||||   | | |||||||| | || ||||||||| || || || ||||||||||| ||||||||||||||||||| | | |    |  |      |  |||  ||||         ||  | ||      | |   | | | || | ||| |        | |   || | |                                                                                   
GATTTGCGTTCATGACAAAGAGTGAAGTGGATCACCTCGACGATGGCTATAGATGGCGCAAGTACGGTCAAAAAGCCGTCAAAAACAGCCCTCATCCAAGgtatatatatatat-atatatatcatatacccatgagtatataattattaatcaatatcaaatatatgcatttcatttatcaaaccttaattcattttgtcattatgattcgttcttctcctttttagtactttggattgggactaataattaaactatttcttgcggtgcacgcaaaacag

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA07G36640.1 (Glycine max), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtct-agttagcaacaagtatctgattaaa----atcgttctgagatatgtgcag--------------------------------------------------
|||||||  |||  ||    |  || |||||   | | |||||||| |  | ||||||||| || || || ||||||||||| ||||||||||||||||||| |  |   |||  |       ||||   || ||| |    ||| |||| ||| | |||          | |||||        || || | ||   | || |                                                   
GATTTGCGTTCATGACAAAGAGTGAAGTGGATCACCTCGACGATGGCTACAGATGGCGCAAGTACGGTCAAAAAGCCGTCAAAAACAGCCCTCATCCAAGgtataccca-tca--atatataattatttgcacatttcattgatcgtcaaatcttaattaattttgtcactttgattctttcttctcctttttagtactttggatttgggttgggactaataattaaaatatttcttgcggtgcacgcaaaacag

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA15G14860.1 (Glycine max), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtt-tgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagat-atgtgcag-
|||||||  |||  ||    | ||| || ||   | | |||||||||| ||| |||||||| || ||||| ||||| || |||||||||||| |||| |||||   | |      ||    | ||| |   ||| || |    | |   |   |||  |    |  |   | |||  | | ||    |  ||| ||    |  
GATTTGCGTTCATGACAAAGAGCGAGGTTGATCACCTAGACGATGGTTATAAGTGGCGCAAGTACGGCCAAAAAGCTGTGAAGAACAGCCCTTATCCCAGgttgcatatcactgtcattt-catttttt-tcattttacaataagccaaataactaaatgttgaggaaagtatgaa-agattcacaatttgattattgataaa

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA09G37930.1 (Glycine max), 5'ss of exon 3
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgt--ttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagtt--agcaacaagtatc--tgattaaaatcgttctgagatatgtgcag
| |||    || ||||  |||  || || ||  |  | || |||||||  |||||| | ||||||||||||||||  |||||||| |||| |||||||||||  |  ||   ||   |    |  | |     || | | |   ||  | ||     |||  |   | || ||    ||| |  |||   | | | | |||     
GGTTTTGTTTCCAAACAAGAAGTGATGTAGATGTGCTTGATGATGGTTACAAATGGAGGAAATATGGCCAGAAAGTTGTCAAGAATAGCCTTCATCCAAGgtaatattcaaatcttgattaaccatgacttttatttgctcattatagtaaacatatgttttaaggaaaaataataatgagttgaattaat-taacacatg-----

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT1G29860.1 (Arabidopsis thaliana), 5'ss of exon 2
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgc-gtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctg-attaaaatcgttctgagatatgtgcag---------------------------
|  ||||  | |  ||   || |||  | ||     | || ||||||| || |||||| |||||||| || ||||| || |||||||||||| ||||||||||  | |  |||| || | |  || |   ||| |        |  | ||  | ||  || ||  | |  | || |  |||||       | ||      |                            
GGGTTGCATTTATGACCAAAAGCGAGATTGATCATCTTGAAGATGGTTATAGATGGCGAAAATATGGACAAAAAGCAGTGAAGAACAGCCCTTATCCAAGgttcatttattcactacactctattcaaatccacacatttataagttacagatatatatatcataatggttttgtaagaaaataaagtgtatattatcataatatcataatttgtttatgcgttttcag

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AT2G44745.1 (Arabidopsis thaliana), 5'ss of exon 3
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgt--ttgtctggtcaccacgcgcgtttatcac-catatt---ccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag
||||     || ||||   || ||| || ||  |  | |||||||| |  |||||||| |||||||| ||||||| |||||||||||||| ||| || ||||  |    | || |     |      | |||  ||||    |  |  |   |  | |    ||| ||| |  |  || ||  ||   || || |  ||       
GATTCTGTTTCCAAACCAAAAGCGATGTTGATGTTCTTGACGATGGCTACAAATGGCGTAAATATGGTCAGAAAGTCGTCAAGAACAGCCTTCACCCCAGgtactaaattagttaattatcatcaccaccacatatatgtgactgcttaggcttcattaactttaccaatagtttcctaatataacatgtccttaattag------

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv15s0021g01310.t01 (Vitis vinifera), 5'ss of exon 3
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctgat-taaaat--cgttctgagatatgtgcag-
| ||     |  ||||  ||| ||| |||||  |  | ||||||||||  |||||| | |||||||||||||||| ||||||||| |||| |||||||||||        | ||  |   |    || |  | ||| || |     |    |     || || ||   ||  |   || |||  |       ||  ||  ||  
GGTTCTGTTTTCAAACTAGAAGCGAGGTGGATGTGCTCGACGATGGTTACAAATGGAGAAAATATGGCCAGAAAGTCGTCAAGAATAGCCTTCATCCAAGgtaac----attactgcctccaaaaataattaaattgcctcataaattttcttatactaacatcatacatagggcatagaatttcccctctggaggtggacaat

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ38698 (Selaginella moellendorffii), 5'ss of exon 1
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatat---tccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag
| |  ||  || | ||||| | ||||||||| |||||||||||||| |||   ||||| || || || || || ||||||||||||||||| ||||||||||  ||  |   |  |   |  ||| ||  |  ||   || ||   | |||     |   | |||                                      
GCTACGCTCTCCAGACGCGCAGCGACGTGGATATCATGGACGATGGATTTCGGTGGCGAAAGTACGGGCAAAAGGCCGTCAAGAACAGCCCCCATCCAAGgtacgtgagcaaaaaaactggatttttcttccgatcgatcaccaagttttctttcttctctcgcag-------------------------------------

upper sequence: PP1S159_105V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: EFJ04574 (Selaginella moellendorffii), 5'ss of exon 1
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcacca--tattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag
| |  ||  || | ||||| | ||||||||| |||||||||||||| |||   ||||| ||||| || || || ||||||||||||||||| ||||||||||  ||  |   |  ||  |  |||    ||      || ||   | |||     |   | |||                                      
GCTACGCTCTCCAGACGCGCAGCGACGTGGATATCATGGACGATGGATTTCGGTGGCGAAAATACGGGCAAAAGGCCGTCAAGAACAGCCCCCATCCAAGgtacgtgagcaaaaaactggatttttcttccgatcgatcaccaagttttctttcttctctcgcag-------------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTGCCATCAAAACGCGAACCGACGTGGACATCATGGACGATGGTTTTAAATGGCGCAAATATGGCCAGAAAGCCGTCAAGAACAGCCCTCATCCAAGgtttgtctggtcaccacgcgcgtttatcaccatattccccccatcttcaagtctagttagcaacaagtatctgattaaaatcgttctgagatatgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC