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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttagtcatctttgatttaattctaaattttttgctcctcatttgagacaagcctgatttttgtatgactttctaaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG

Basic information

species Glycine max
transcript GLYMA08G44580.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 6
----------gtactt-agtcatctttgatttaattctaaattttttgc------tcctcatttgagacaagcctgatttttgtatgactttctaaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG
           || || |   |  |||| | |   | | | | |||||       |  |   ||         ||    ||| ||  | |   | |  |||| ||||| ||||| ||||||||||||||||| ||||| ||||| || || |||||  ||||||| || ||||| || |||
tcaaagctaaatattttaaatagttttgttgtggatgtcattcttttgggtaggatatttccttttacttcatctatagtttataaaattgatttatcagGTTAAGCAGATGGTTGTTGCTACACTTGCTGAGTCTGGAATGAATCTTTCTGATGAAATTATAGAGAGCATAATCGATAAG

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 6
--------------gtacttagtcatctttgat-ttaattctaaattttttgctcctcatttgagacaagcctgatttttgtatgactttc--taaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG
               |   |  | ||     ||   |  | |  |||   |  |   | |||  | | ||||| | |  |  ||  | ||   |    |||| ||||| ||||| ||||||||||||||||| || || ||||| || ||||||||  || |||| |||||||||||||||
cttttttctgaagtatttctcttgataagaaatgccacctttggattgaattatgtccttttttggctagccttaatggttaattgcgtttggttttcagGTTAAGCAGATGGTTGTTGCTACACTTGCTGAGTCAGGAATGAATCTTTCAGATGAAATTGTAGAGAGTATAATTGACAAG

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 6
----gtacttagtcatctttgatttaattctaaat---tttttgctcctcatttgagacaagcctgatttttgta-----tgactttcta--aatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTAT-CAG-ATGATGTTATAGAAAGTATAATTGACAAG-----------------------------------------
    ||  ||  || |      || |  |   ||    | | | |   | || |||      | || |   ||||     |||  |   |  || || |   |  ||   |  ||   |   | | |  | ||   |||| | ||  ||| | | | | ||||| ||   |   |  |||                                         
gtacgtctttgatcttacaaagttgatctgagaaaccatctatacaatttatctgatgttgacatgctacatgtaacccatgaaatatcactaacagttaccgggaacattgttttgcagTTTCGTTTCAGCTA-TATGATCTTAAGCAGCAAGGTTTCATAGAGAGGCAAGAGGTGAAGCAAATGGTGGTGGCTACTCTTGCTGAGTCCGGCATGAACCT

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 7
---gtacttagtcatctttgatttaattc-----taaattttttgctcctcatttga--gacaagcctgatttttgtatg-actttctaaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG
      |||    |||||  | |   |||     |||  || | |     |  || |    |    ||||  |||   |  |   | |    ||||||| |||||||| || ||||| |||||||||||||| |||||  |    |||  ||| || ||   |||||| ||||||
gtaaagcttccatatcttcaaatagcttcatatataaccttgtagaagtgcgctttattatcctcactgacattttcgtccatcatttgtccagGTGAAACAAATGGTTGTCGCTACGCTTGCTGAATCTGGAATGAATTTGAAGGATACTGTCATTGAGGATATAATCGACAAG

upper sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 5
---------gtacttagtcatctttgatttaattct-aaattttttgc---tcctcatttgagaca--agcctgatttttgtatgactttctaaat--agGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG
          | ||| ||  | |     |   ||||   | ||| |     | ||| ||||  |    ||      || | | |||| | ||| ||  ||||||||||||||||||| || ||||||||||||||||| ||||| || || |||||||||||||||||||| |||||||||
atttgtaggttgcttggttttatccctctattttcttggactttctataatttctcttttgtcattttagttcttcttgtatgtgacctcctatatttagGTGAAGCAAATGGTAGTGGCCACACTTGCTGAATCTGGTATGAATCTTTCGGATGATGTTATAGAAAGTATCATTGACAAG

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|213597200|gb|DB981592.1|DB981592
EST:     CCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGGCAAGAG                         GTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCA
genomic: CCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGGCAAGAGgtacttagtc ... ttctaaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCA
EST: gi|209710674|gb|BW671020.1|BW671020
EST:     CCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGGCAAGAG                         GTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCA
genomic: CCTTTCAACTATATGATCTCAAGCAGCAGGGTTTTATTGAAAGGCAAGAGgtacttagtc ... ttctaaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttttgctcctcatttgagacaagcctgatttttgtatgactttctaaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG
                                           ctttct  CT-rich tract
                               atttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttagtcatctttgatttaattctaaattttttgctcctcatttgagacaagcctgatttttgtatgactttctaaatagGTGAAGCAAATGGTAGTTGCTACACTTGCTGAATCTGGCATGAACCTATCAGATGATGTTATAGAAAGTATAATTGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG