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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtgtgttgagttgataatgatgacattggtacataaaatcattcttgtgctactattatcttctctgtatgtcactgatagttcttgagttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC

Basic information

species Glycine max
transcript GLYMA17G00830.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g42840.1 (Oryza sativa), 3'ss of exon 6
-----tgtgtgtgttgagttgataatgatgacattggtacataaaatcattcttgtgctactattatcttctctgtatgtcactgatagttcttgagttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC
     |   | |||  | || | ||   ||||  | ||   |   ||  ||  | |  | ||      || | | |||     | ||| | |     |||   ||||||||||||| || || || |||||||||||||| ||||| || ||||||||||| || || ||  |  | ||||| ||  | |||||||| ||||| |
attgctacctttgtacattttacaa-actgac--tagttgctgtgattgtttatattattctggctgtttatat-tattatgtttatattgcacattttaca-agACATTTGAGGAGGCCGACACAAAACATGATGGGAAAATTGATAAAGAAGAATGGCGCAATCTAGTTCTCAGACATCCTTCTTTACTGAAAAACATGACAC

upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G112672_T02 (Zea mays), 3'ss of exon 6
-tgtgtgtgttgagttgataatgatgacattggtacataaaatcattcttgtgctactattatcttctctgtatgtcactgatagttcttgagttattta---gACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC
   | |   || | |  ||| |    |||   | | |    |  | |  ||  |  |   | |  | | || || | | | |  ||| ||   || | ||   ||| |||||||| || || || || ||||||||||| |||||||| ||||||||||| ||  | ||  || ||||||| ||  |  |||| || ||||| |
gcttattacttaaataaatactccaaacaagtgaaaacgtgacaagt--tggtcagcctatgtgctatttgaatcttattaa--gttttttctttttctaaaagACTTTTGAGGAGGCAGACACAAAGCATGATGGGAAAATTGACAAAGAAGAATGGCGCAATTTAGTAGTGAGGCATCCCTCTTTATTGAAGAACATGACAC

upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G26570.2 (Arabidopsis thaliana), 3'ss of exon 7
tgtgtgtgttgagttgataatgat-gacattggtacataaaatcattcttgtgctacta--ttatcttctctgt--------atgtcactgatagttcttgagttattt-------agACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC
 |||||  |       |   || | || | |      |     || | ||||    | |  | ||  |  | ||        | || |    | |||  | ||||  ||       |||||||||||||||||||||| |||||||| |||| ||| || |||||||| ||| ||| ||||||  |  ||||||| |||||||| || ||||||||||
-gtgtggttccttcctaccctgctcgatactatattcttgttccactgttgtatagccaactcatgatagcagttgagaataaagtaaagagtggtttctaagtttcttctttcacagACATTTGAGGAAGCTGATACAAAACATGACGGGAGGATCGATAAGGAAGAGTGGAGAACCCTTGTTCTCAGGCATCCTTCCCTTCTAAAGAATATGACTC

upper sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 6
tgtgtgtgttgagttgataatgatgacattggtacataaaatcattcttgtgctactattatcttctctgtatgtcactgatagttcttgagttattt-agACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC
  | |   |||  |||  |   ||    || | |    ||| |||  || |  | | || | ||||    ||| |   | ||| |  |    |||||| |||| ||||||||||||||||| ||||||||||||||||| ||||||||||||||||||| |||||| ||||| |||||||| ||| |||| |||||||| |
gatattgattggattggaatgaatatttttagcattccaaa-catatttatcttgcaataagcttcctattatatttttaatattcttatttttatttcagACCTTTGAGGAAGCTGATACTAAACATGATGGGAAGATAGACAAGGAAGAATGGCGAAGCCTTGTTTTGCGACATCCATCTCTTTTGAAGAATATGACCC

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|21285464|gb|BQ473335.1|BQ473335
EST:     TTTCAGATGATGTGATCGAAAGTATTATTGACAAG                         ACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA
genomic: TTTCAGATGATGTGATCGAAAGTATTATTGACAAGgtgcttcatt ... agttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA
EST: gi|15812919|gb|BI785194.1|BI785194
EST:     AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAG                         ACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA
genomic: AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAGgtgcttcatt ... agttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA
EST: gi|19054016|gb|BM732683.1|BM732683
EST:     AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAG                         ACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA
genomic: AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAGgtgcttcatt ... agttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA
EST: gi|151412447|gb|EV282259.1|EV282259
EST:     AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAG                         ACATTTGAGGAAGCTGATACCAAACATGATGGGGAAGATTGACAAGGAAGA
genomic: AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAGgtgcttcatt ... agttatttagACATTTGAGGAAGCTGATACCAAACATGATGGG-AAGATTGACAAGGAAGA
EST: gi|193402920|gb|FK367242.1|FK367242
EST:     AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAG                         ACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA
genomic: AATCTGGCATGAATCTTTCAGATGATGTGATCGAAAGTATTATTGACAAGgtgcttcatt ... agttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtgctactattatcttctctgtatgtcactgatagttcttgagttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC
                              cactgat  putative branch site (score: 3)
        tactattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtgtgttgagttgataatgatgacattggtacataaaatcattcttgtgctactattatcttctctgtatgtcactgatagttcttgagttatttagACATTTGAGGAAGCTGATACCAAACATGATGGGAAGATTGACAAGGAAGAATGGCGAAACCTTGTCTTGCGGCATCCATCCCTTCTGAAAAATATGACTC

-gtgtgtg
- - - - - - - - - - tgatgac
- - - - - - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcttg