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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG

Basic information

species Glycine max
transcript GLYMA10G43230.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 3'ss of exon 5
gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataat-tcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
    ||||     | | |   ||  ||    | |  ||   |    |     |  || || |||     |   ||  || |||| |  |  | ||||  |||||||||||||||||||| ||||| || || ||||| || || |||||||| |||||| | ||||| |||||  |||| |||||  |||||||  || | 
-tgttttttgaggtcatttttttaattgatgtcatttttaattataccatggtatatattgattatatgaatgaaggatgtcttctttttaatatatatagTGGTGAGAGTGGAGCAGGAAAGACAGAAACTGCAAAGATTGCTATGCAGTATTTGGCTTCTCTTGGAGGTGGGGGTGGCATAGAATATGAGATCCTACAA

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 5
----gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
    |   |||     ||| ||  | |   | |  ||   | |    |    | |||   |    |   |    | |  | |||||||| || |  |||  ||||||||||||||||||||| || || || || |||||||| || ||||||||| ||||| ||||||| ||||||||||| || ||  | || ||  |  ||
tgaggtcatttgggaaattgatggcattaatattctag--tagcacccttactgattatgtgaagacgtgatgccgttttgattcttttgattttgata--cagTGGTGAGAGTGGAGCAGGAAAAACAGAAACCGCAAAAATTGCTATGCAGTACCTGGCTTCCCTTGGAGGTGGAAGTGGCATTGAATACGAAATTCTTCAG

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 5
---gaagttttcagca-ttaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
   ||   ||| || | || || || |   | |  ||   | |    |   || ||| | |    |   |    |||  | |||||||| || |  |||  ||||||||||||||| ||||| || || || || || ||||| || ||||||||  ||||| | ||||| ||||||||||| || ||  | || ||  |  ||
tgagatcatttgagaaattgattacattaatattctag--tagcacccttattgattacgtgaagaggtgatggcatttttattcttttgattttgata--cagTGGTGAGAGTGGCGCAGGAAAAACAGAAACTGCGAAAATTGCTATGCAGTATCTGGCTTCTCTTGGAGGTGGAAGTGGCATTGAATACGAAATTCTTCAG

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 6
---gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
   |    | |    | || |   || |||     ||     | | || |||  | |||| || |   |    | ||  |     |||| | | |||   |||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| ||||| ||||||||||| || ||| |||||||| |||||
agtgcgactatggaaaatagtggattggttgaaagaatgagttcttccactttgt-gcatcttgaagtgttttcttatcacaagatttctttttcat--ccagTGGAGAGAGTGGAGCAGGAAAGACTGAGACAGCAAAGATAGCGATGCAATACTTGGCTGCTCTTGGAGGTGGAAGTGGGATCGAGTATGAGATACTAAAG

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 7
-------------------gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
                   ||     | || | || |   |  |||   | ||  | |||   ||  |   || |||||     | |  | ||  |     ||  || |     | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || ||                   
gtaaagttgcattagttgtgagacactgag-actagtggatctgttgaataaag-tggtgcttccagtttgtgtattttgtggtgtatccttatcacaagATTCTATTTCTTCTTCCAGCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGAT-------------------

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 6
--gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
  ||     | || | || |   |  |||   | ||  | |||   ||  |   || |||||     | |  | ||  |     ||  || |     | ||| || ||||||||||||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| || ||||| || || ||  |||||||| | |||
gtgagacactgag-actagtggatctgttgaataaag-tggtgcttccagtttgtgtattttgtggtgtatccttatcacaagattctatttcttcttccagCGGCGAGAGTGGAGCAGGGAAAACTGAGACTGCTAAAATAGCTATGCAATACTTGGCTGCTCTTGGAGGCGGAAGCGGGATCGAATATGAGATACTTAAG

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 5
-gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
   |   |   |   ||  || ||      | | |  | ||  |       |||| |||  |     || | ||  ||| ||  ||| | |     | ||||||||| |||||||||||||| |||||||||||||| ||||||||||| || ||||||||||||||||| || || ||||||||  |||||||||| || 
cttaaaatcgggttatatcaagttgagaaccctgaattggttagtaaaactattgtattgaatccttgataaatc-taaatcaattcttttgttcttccagTGGTGAAAGTGGAGCAGGGAAAACTGAGACGGCAAAGATAGCAATGCAATATTTGGCTGCCCTTGGTGGCGGTAGCGGAATAGAATATGAGATATTGAAA

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S104_215V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------gaagttttcagcattaataacttc----gttttcttaaccttgtgtgccccttaattgcattttaattgggacacat--------aataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
                                                     |  |||| |   | || ||   |     | | | |    ||     |   ||| | | ||| |  |       |||        || ||     ||  | |   | | ||||||||||||||| |||||||| || || |||||||| || || |||||||| || ||||| || || || || ||||| |||||  |||| || ||  | 
gtaatttgtatatctttgttctacattttgttctgttccaaagaagaatctcaatttttttaatttaaagaatggccggaatctgcatttatttaaacactagttattagtattctcttcaatggtcatctcatgaaaacaacatgcttattttttgtgtacagTGGTGAGAGTGGTGCAGGGAAAACAGAAACGGCAAAGATTGCCATGCAGTATTTAGCTGCTCTAGGAGGAGGTAGTGGGATAGAAGATGAAATTTTGCAA

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------gaagttttcag--cattaataacttcgttt--tcttaacc----------ttgtgtgcccctt--aattgcattttaattggga--cacataata---attcttttcat-ctac-atattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
                                | ||||||    |  | || |||| |||  | | || |          |||||      ||   |  |  |  |  | |  |   | || ||    |   |||||||  |||  | | ||||||||||||||| ||||| ||||| || |||||||| || || |||||||| |||||||| || || || || |||||||||||  |||| || ||| | 
gtagtttatgtcccttgattcggtgctatattaattttcaaactacgagtatcttcttttgttttcaatcagcgaccacgttgtgcatttatttagacagtgtcctcttcgatagctatatgatgtacacggttttcatattactgtgtacagTGGTGAGAGTGGCGCAGGTAAGACAGAAACGGCAAAGATTGCTATGCAGTATTTGGCTGCTCTAGGAGGAGGTAGTGGAATAGAAGATGAAATTTTACAA

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 4
gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
                                        ||  |  |||  | ||| | | ||        |  | || |||     | |    | ||||||||| ||||| || || || |||||||| || || || ||||||||||| || ||||||||||| |||||| | ||  | || ||||| ||| |  | 
----------------------------------------gtaacgattatctacatgt-attttactggttttcttatactt----gcaatgcttgcagTGGTGAAAGTGGGGCCGGCAAAACTGAGACTGCGAAGATTGCAATGCAGTATTTAGCTGCCCTTGGAGGTGGAGGAGGTGTGGAAAATGAAATACTGGAA

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ20281 (Selaginella moellendorffii), 3'ss of exon 4
gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
                                        ||  |  |||  | ||| | | ||        |  | || |||     |||    | ||||||||| ||||| || || || |||||||| || || || ||||||||||| || ||||||||||| |||||| | ||  | || ||||| ||| |  | 
----------------------------------------gtaacgattatctacatgt-attttactggttttcttatactt----gctatgcctgcagTGGTGAAAGTGGGGCCGGCAAAACTGAGACTGCGAAGATTGCAATGCAGTATTTAGCTGCCCTTGGAGGTGGAGGAGGTGTGGAAAATGAAATACTGGAA

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ05534 (Selaginella moellendorffii), 3'ss of exon 4
gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
                                      ||| |      | |||| |   | ||  |  |   | |  |||  | |   ||| | |||||||| |||||||| || || ||||| || || ||||||||||| ||||||||| | ||| |  ||||||| ||| ||||  ||||| |||| ||  |  | 
--------------------------------------gtgagg-----agttgcctggaatttatgtgatgcactgtttcaatgctgatac-ttttcagTGGCGAGAGTGGTGCTGGAAAGACGGAAACAGCAAAAATAGCTATGCAGTACATCGCTACATTTGGTGGAGGACGTGGCGTAGAGGATGAAATCCTTGAA

upper sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ25955 (Selaginella moellendorffii), 3'ss of exon 4
gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
                                      ||| |    ||   || | ||||  || ||  |||  |  |||  | |   ||| | |||||||| |||||||| || || ||||| || || ||||||||||| ||||||||| | ||| |  | ||||| ||| | ||  ||||| |||| ||  |  | 
--------------------------------------gtgaggat-ttgcctggaattta--tgtgatgcat--tgtttcaatgctgatac-ttttcagTGGCGAGAGTGGTGCTGGAAAGACGGAAACAGCAAAAATAGCTATGCAGTACATCGCTACATTCGGTGGAGGACGGGGCGTAGAGGATGAAATCCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG
           ttttaat  putative branch site (score: 3)
                                 ttcttttcatctac  putative PPT
                          ataataattcttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagttttcagcattaataacttcgttttcttaaccttgtgtgccccttaattgcattttaattgggacacataataattcttttcatctacatattcagTGGTGAGAGTGGAGCAGGGAAGACTGAGACGGCAAAAATAGCAATGCAGTACTTGGCTGCCCTTGGTGGTGGAAGTGGAATAGAGAATGAGATATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - ccttgtg
- - - - - - - - - - - - - - - - - - - - -tgcccct
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacata