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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG

Basic information

species Glycine max
transcript GLYMA02G46780.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
--tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaa---cagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
  |   | |  || ||||    |||  |  |   | |||||     |   || || | | |||   || |||   || ||  |   |  ||| |   ||   |||||||||||| | ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||||||
tctgtgaataatcagaaacagcttctgttca--ttacttat---cccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 10
tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
                |   || |  ||  ||  ||| |    | ||     | ||   |  ||   ||| ||    || |  | |||  |  |   ||||| ||||| || |||||||| || || || |||||||||||||||||||||||||| || ||||||
---------------gtatgttgctggttgtcctcttctttactttattttttctctcctgctc---tcttgaaaggttgtctaatttctctccatgcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATATTTGATGAAAACGATTCAAAG

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 10
tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
           |     ||  ||  | |  | ||||| |    |||  |   |      ||| | |||||   | || || | ||||     |    ||||| ||||| || |||||||| || || || |||||||||||||| ||||||||||| || || || 
----------gtatgtgccgctct-tcttttgtgcttctttactctctctcttccacagttagctaatct--ctttcctactaatttgtttct---gcagATAGTAACTCTTGAAGATGTGGTCGAAGAGATTGTTGGTGAAATTTTTGATGAAAACGATTCCAAA

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 10
----tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgat-tttgccatct-aacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
    |   ||  || ||  | | || | |  |  |||   |  |  || | | |   ||| ||   ||| | |   || ||||  | || ||| |  | | ||||||| ||||| || |||||||| |||||||||||||| |||||||| || ||||| ||||| ||||| 
atattatgagatttatgcca-ctatccaacatcctctttgtgcacttttttata---ttctgt--gtcagaaccttatttcttccttatcttttctgtatgaacagATAGTAACCCTGGAAGATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAA

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 3'ss of exon 12
-tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaa--ctttcagtttatcaaatctagatgtcttattgattt-tgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
 |  |||     | || |  | | ||   | ||    |  | ||| ||  ||   |||   ||| |  |||| | |    | | ||||     |    | |||| |||| ||||| ||||||||||| || || |||||||| ||||| |||||||||||||| || |||
ttgtaagggggattaattttaattca---actccaagttgaggttgtagtaaattttttgttttgtgcaatcaatacaaat-actgatgaacacagaattacagGTTGTGACACTGGAAGATGTTGTGGAAGAGATTGTTGGCGAAATTTTTGATGAAAATGATTCCAAG

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 3'ss of exon 13
--tccaagtc--ttctgaaatccattccatgt-aatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
  | ||| ||   | | ||||  |  |  |||  |     ||   | || |||  | |   | |  | | |  |||      ||      |  |  || |   || ||||||| || ||||||||||| || || |||||||| || || || ||||||||||| ||||||
acttcaattcaactttaaaattaaggctgtgttgaatcatttgatatttgtaatcaatacaaat--accgatgctaacaaagttgcaccatgcgttattt---agGTTGTAACGCTGGAAGATGTTGTGGAAGAGATTGTTGGGGAGATTTTCGATGAAAATGATTCAAAG

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S58_81V6.1 (Physcomitrella patens), 3'ss of exon 13
-----------------------------------------------------------tccaagtcttctgaaatccattcca--tgtaatct----gcttataagtt-ctaacaactttcagtttatcaaatctagatgtctt---attgattttgc------catctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
                                                             ||| |     | | || ||| ||  |||||       |||||||| |  |   |  |||||      | | || |  ||        | | | ||| |      |    | ||| |||| ||| | ||||| |||||||| ||||||||||||||||| |||||||||||||| || |||
gtaagatttgaaaagcacatgacaactaatctgatagaatatttatagtctctgttgtgagcaatttcaagggagtctatttcaactgtaagaatagggcttataattagccccctgctttcctcacttgatatttgaatactaatggaatcaatttacgtgatacgctcaccagGTTGTGACATTGGAAGACGTTGTTGAAGAAATTGTTGGTGAAATTTTTGATGAAAATGATTCGAAG

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ38618 (Selaginella moellendorffii), 3'ss of exon 10
tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
                                      || |||  |     |   ||||  |    |   |  || | ||  | ||     | |  |||||||||||||| ||||||||||||||||| |||||||| ||||| ||||| ||||| || || |||
-------------------------------------gtacgtttcatatcttcgtagttctt----ttcgggagtataatacacttc----tattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG

upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ31527 (Selaginella moellendorffii), 3'ss of exon 10
tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
                                                 |  |||||  |  |    |   |  || | ||  | ||     | |  |||||||||||||| ||||||||||||||||| |||||||| ||||| ||||| ||||| || || |||
-----------------------------------------------gtacgtttca--tagttcttttcgggagtataatacacttc----tattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG
                                       ttttgcc  CT-rich tract
                                ttattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaacagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG

- - - tcttctg
- - - - - - - - -ccattcc
- - - - - - - - - - - - - - - tctgctt