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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttttttgttacgttttttattctttcctgaccgcgtatactggcttgtacttttccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG

Basic information

species Glycine max
transcript GLYMA17G34610.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 5
acttttttgttacgttttttattctttcctgaccgcgtatactggcttgtacttttccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
  |   | |||| |    | | |  |    |               ||   |   | | |||  | |  |  |  | |  |  |  |||| |  |  ||||| ||||| ||||||||||| || || || ||||| || || || |||||||| ||||||||||| || || |||||||| || ||||||||||| || |
tatgcatcgttaagcccataaatggtgtgaggatttacccctcattttcatcacatgcatatgttatacggcaaatgacaagctgcttccttgttttcagCGTTTTACACGTCTTGGTGGAAAACTGCCAAAAGGTGTCTTGCTGGTTGGTCCTCCTGGCACTGGAAAGACCATGTTAGCAAGGGCTATTGCTGGGGAAG

upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g39250.1 (Oryza sativa), 3'ss of exon 5
--acttttttgt-tacgttttttattctttcctgaccgcgtatactggcttgtacttttcct-tatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
  |||||  ||  ||  |  | |||  |||| | || |  |    || | | ||||| | || |||  |  |   || |  |  |  |   ||| |  |  ||||| ||||||| ||||||||| || || || ||||| || || || ||||| || |||||||||||||| || |||||||| || ||| ||||||| || |
gcactttaatgcatatatgatctatcatttcataactgttt---ttgtcatatacttgtgctatatggtgatcagaagtc-acaagctgcctccttcttttcagCGTTTTACTCATCTTGGTGGAAAACTGCCAAAAGGTGTCTTGCTGGTTGGCCCTCCTGGCACTGGGAAGACCATGTTAGCGAGGGCTGTTGCTGGGGAAG

upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 5
acttttttgttacgttttttattctttcctgaccgcgtatactgg---cttgtacttttccttatcatctttgtaat-tttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
    |  | ||| |    | ||    || ||||  |   |   ||   ||| |  ||    || || |   | | ||  | |  |  | |   | |  |  |||||||| || ||||||||||| || |||||||||||||| || ||||||||||| ||||||||||||||||| ||| ||||||| ||||||||||| || |
----tgcttttatgaagctcatctcgtcttgacaacacctggaggtaccttatttttcattttgtctttcgtatgatgctcacaaactgtgctcttgttttcagCGCTTCACACGTCTTGGTGGAAAACTTCCGAAAGGAGTCTTGCTTGTTGGTCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG

upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G463032_T01 (Zea mays), 3'ss of exon 4
acttttttgttacgttttttattctttcctgac-cgcgtatactg-gcttgtacttttccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
     |    || | || |  | |  || | || | ||   |  |  || ||  | ||   | |  |  |   |   | |  |  | |   | |  |  |||||||| ||  |||||||||| || ||||| ||||| || || ||||| || || ||||||||||||||||| ||| ||||||| ||||||||||| || |
-accatcaaatatgattgt-gtgccgtcgtaacacacgggcatcgtactagtcttattatatgtttttataagatgctcacaaactgtgctcttattttcagCGCTTCACATGTCTTGGTGGAAAACTTCCTAAAGGTGTCTTGCTTGTGGGCCCTCCTGGCACTGGGAAAACCATGCTAGCTAGGGCTATTGCTGGTGAAG

upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------------------------------------------acttttttgttacgttttttattcttt------cctg-accgcgtatact---ggcttgtact-tttccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
                                                                                  |  || |  |   |   ||||| || |       |||  ||  || |       | | ||||| |||  || | |    |  | | ||    |||||   | ||   | || | || |||||||| || || |||||||| || || || || ||||| ||||| ||||| || || ||||| ||| | |||||||||||||||||||| |
gtaaattcacagtgctagagtgtttttctagttaagtataaaatctgtctagtgatgtaaattcaaaagcataaatcatgtgaagttatcatatagacctttatcctctgaattatctgtgccaggtttttctagagttagtactgttttgttcttaggcct-cactctttcatcttttgatctttactatagAGGTTCACTCGTCTGGGAGGAAAGCTTCCTAAGGGTGTGTTGCTTGTCGGTCCTCCTGGGACAGGAAAAACTATGCTTGCTAGAGCTATTGCTGGAGAAG

upper sequence: GLYMA17G34610.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 5
--acttttttgttacgttttttattctttcctgaccgcgtatactggcttgtactttt---ccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
  |   ||   | |  ||      |    |||||   | |||      ||  | || |    || |  |  ||| | ||||||||     |||||||||| ||||||||| |||||||| ||||| || ||||| || || ||||| |||||||||||||||||||| || || || ||||| || |||||||| |||||||| |
aaaaacttccatgaaattaaaatgtaaaccctgaagccctatctctagttagagttgtatatctgaataggtttcttattttatg-----tttcccttgttacagCGCTTCACTCGTCTAGGTGGCAAACTTCCAAAGGGTGTTTTGCTTGTTGGTCCACCTGGCACCGGCAAGACCATGTTGGCAAGAGCTATCGCTGGAGAAG

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|207694162|gb|GD675153.1|GD675153
EST:     AGGCAAAGGAAGAGCTGGAAGAAATTGTTCACTACCTTCGAGATCCAAAG                         CGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGT
genomic: AGGCAAAGGAAGAGCTGGAAGAAATTGTTCACTACCTTCGAGATCCAAAGgtagacatgt ... cttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGT
EST: gi|208265124|gb|GE064430.1|GE064430
EST:     AGGCAAAGGAAGAGCTGGAAGAAATTGTTCACTACCTTCGAGATCCAAAG                         CGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGT
genomic: AGGCAAAGGAAGAGCTGGAAGAAATTGTTCACTACCTTCGAGATCCAAAGgtagacatgt ... cttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtacttttccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG
                                    cttttttcccttgt  CT-rich tract
                     tttgtaattttatgac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttttttgttacgttttttattctttcctgaccgcgtatactggcttgtacttttccttatcatctttgtaattttatgacttttttcccttgtgacagCGCTTTACTCGTCTTGGTGGTAAGCTTCCGAAAGGAGTTTTACTTGTTGGTCCACCTGGCACTGGGAAAACAATGTTAGCTAGAGCTATTGCTGGAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - tcctgac
- - - - - - - - - - - - - - - - - - - - - tggcttg