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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

Basic information

species Glycine max
transcript GLYMA20G24790.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 7
-------------------------------taaaagataatcaacaaaatctattttctagg---ctattgttatagtagtagttttatttggt--gtaaatgt-gcatctcagttctaccttatcttca-----ttgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
                                   | |||||  | |  || | ||| | |      || ||||    |  |   |    ||| |     | ||| | |   | |   | | || | |         || |||| || ||||| || || ||||||||||||||||||||  |  | ||||||||||||||||| || || || || || ||||||||||| |||||||| |
gtcacaagcaaaatatcttcataaaattttacttgaaataattcaaattatttgtttgcaacagctttactgttcagttgtttactaccattgcttcacgattgttggaaacctgacttgctttgtttctggcattctgtagGAGGCTACAATCGAACAACTTCTTCCTATTTTCCTTTCTTTGCTCAAGGATGAATTTCCTGATGTTCGGCTCAATATAATCAGCAAGCTCGATCAAGTTA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
taaaagataatcaacaaaatctattttctaggctattgttatagtagta--gttttatttggtgtaaatgtgcatctcagttctaccttatcttcattg-cagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
                | |||  |  |  |  |   ||||     | ||  || ||      |||  |  | |     |     | | | ||||| ||| ||||| || || ||||| |||||| |||| |||||||| ||  | ||||| || ||||||||||| || || || ||||| |||||||| ||||||||||| |
-------------gtgatatcagtgatgcaaacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 7
taaaagataatcaaca-aaatctat-tttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
    | || |   |   | |  ||| |||| |   ||| ||  |  || |  |   |||   |||||  |   |||  | |  |||||| | ||    |||||| || || || || ||||||||||| ||||| || ||  |  |||||||||||||||| || || || || ||||| ||||||||||||||||| || |
-gtgatatcagtgatgcagacttatgtttcaattatatggtgttgatactgttggcattccatgtaa--gctgatcgtattaataccttttttttg--gcagGATGCTACCATGGAACAGCTTCTTCCAATTTTTCTCTCTTTGCTGAAGGATGAATTTCCAGATGTTCGGCTTAACATAATCAGCAAGCTTGATCAGGTTA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 6
taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttgg--tgtaaatgt---gcatctcagttctaccttatcttc---attgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
      | ||  ||   | | || ||     ||  || |||||   |  |||||  ||||  |||  ||||     || | |  |  || || | ||    |||  |||| |||||||||||||| || ||||| || || ||||| || ||||| ||||| || || || |||||| | |||||||||||||| ||||| |||||||
------acaa--aaatgagtttaattgacgtgcgtttcttatacaggatgttttggttggattgtgtatgttgcagattttaacttcacgttgttttttctattttagGATGCAACAATTGAGCATCTCCTTCCAATCTTTCTTTCTCTATTGAAAGATGAGTTCCCGGATGTACGCTTGAACATTATCAGCAAACTTGACCAAGTGA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------------------------------taaaagata--atcaacaaaatc---tattttctaggctat--tgttatagtagtagttttatttggtgtaaatgtgcatctcag-----ttctaccttatc-------ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
                                                               | |  | |   ||||||||||||    ||    |  | |||   ||  |  ||  ||    |  ||||||    |  | | |||      |  || | ||         |||| | |||||  |||| |||||||| ||  | || ||||| |||||||||||||| |||||||||||||| || ||||| ||||| || |||||| | |||||||| |
gtatgaactgaagatagccaacattttcgcatcttgtgacaatgttctgagatttaatttgttttatggttttcatcaacaaaatcagccataccttgtgttatggcgtggttataccagccccaactggtgttgcagaccttatcaaaaaattattaacatactaaaatctttcaatacagGACTCAACCATTGAGCATCTGTTACCAATTTTTCTTTCCCTTTTGAAAGATGAATTTCCTGATGTGCGCCTTAACATCATAAGCAAGTTAGATCAAGTCA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 7
-taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgca--tctcagttctacctt-atcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
   ||  |||||| | | ||   |   ||    |||| ||| |  ||       ||||| ||   | | ||||  | | |  |   | || || |||||| ||||| |||||||||||||| |||||||| || || ||||| || ||||| || ||||||||||| |||||| |||||||||||||||| ||||| |||||||
cgcaacaataatctatataagaaaacctc---actat-gtttttctacacaagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 6
taaaagataat-caacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttc-attgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
 ||  |||    |||   ||  |  ||   ||   ||| || |  ||    |  | |||  || || ||    ||| |  | |  |||   | |   ||||||| ||||||||||| || |||||||| ||||| ||||| |||||||||||||| |||||||| ||||| ||||| || || ||||||||||||||| | |
caattgatctcacaattcaaatttattgggagtgcatttttctgttaa-gatcatgtttcttg-aattggatttctgaactttgtcttggttgctgatgcagGATGCAACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 6
-taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctacctt----atcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
  |||   |        |  |||   | ||    | ||  |||     ||    | |     || | | ||||| ||| |    | ||    ||| |  ||||||||||| || |||||||| ||||| || || || || || || ||||||||||||||||| || || || ||||| |||||||||||||| ||||||||||
tcaaactttggattgatatttctgcatcct----tcttaatatctgcataagcctctcaaaagtga-tctgcatttcaatgtatcttttggcatcatttttgcagGAAGCTACCATTGAGCAACTTCTGCCCATATTTCTGTCACTGTTGAAGGATGAATTTCCAGATGTGCGACTAAATATTATCAGCAAGCTAGATCAAGTGA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 3'ss of exon 6
taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcat---tgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
      |||||    |||||   ||   |   | | ||      ||     |  | |  | |  || ||| |  || ||  | | ||   || ||   |||||||||| || |||||||| ||| | || || ||||| || || ||||||||||||||||| ||||| || ||||| || ||||||||||| |||||||| |
-gttttataatttttaaaatt--ttccatgaccaactgagtatatatgctatccaatgagagacaacgtgtaattccgtgttgctttggttttatctatgcagGAAGCTACTATTGAGCAACTTTTACCCATATTCCTATCACTGTTGAAGGATGAATTTCCAGACGTGCGGCTAAATATCATCAGCAAGCTAGATCAAGTCA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ35758 (Selaginella moellendorffii), 3'ss of exon 6
taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
                                              ||||    | || |||    | |      | || ||   |  | |   |||||||| || ||||| || |||||| | || || ||  |  ||||||||||||||||||| ||||||||  | || ||||| || |||||||| |||||||| |
----------------------------------------------gtagg--caattcgtgc---tctttcgtcctgtgctgattagtttggtttgcagGACGCGACAATCGAACAGCTTTTACCAATATTTTTGGCCCTTTTGAAGGATGAATTCCCTGACGTTAGGCTCAACATCATAAGCAAGCTGGATCAAGTCA

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ10709 (Selaginella moellendorffii), 3'ss of exon 6
taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
                                              ||||    | || |||    | |      | || ||   |  | |   |||||||| || ||||| || || ||| | || || ||  |  ||||||||||||||||||| ||||||||  | || ||||| || |||||||| ||||||    
----------------------------------------------gtagg--caatttgtgc---tctttcgtcctgtgctgattagtttggtttgcagGACGCGACAATCGAACAACTTTTACCAATATTTTTGGCCCTTTTGAAGGATGAATTCCCTGACGTTAGGCTCAACATCATAAGCAAGCTGGATCAA----

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|207745402|gb|GD715448.1|GD715448
EST:     GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: GGTCTGCTTTGGCTTCAGTAATAATGGGAATGGCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
EST: gi|9205515|gb|BE331739.1|BE331739
EST:     ATGGCTCCAGTGTTGGGAAAG                         GAAGCAACAATTGAGCAGCTCCTTCCTATTTTCCTTTCCCTTTTGAAGGAT
genomic: ATGGCTCCAGTGTTGGGAAAGgtataagtgt ... ttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
                                 ttctaccttatcttc  CT-rich tract
     ttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgcatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
-aaaagata
- - - - - - aacaaaa
- - - - - - - - - - - - - - - -gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatct