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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

Basic information

species Glycine max
transcript GLYMA03G16660.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G850355_T08 (Zea mays), 3'ss of exon 8
----------ttatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
          ||| |   | ||        || ||  ||| |    |   || || | | |    |  ||| | |||  ||    ||  | | || ||  || |||||||| |||||||||||||||||| |  ||||||| ||||| |||||| |||| |||||
agtgtaagatttagagcccattaccacccctgtgtgccataacagatcattctttccttctgatttcacatct-tatatttataatatgttttca-ttgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G115948_T01 (Zea mays), 3'ss of exon 5
---ttatatt-tctttgaatgatttgagttgcattagttttacctcatttcat--tttccctatcatttc-tatggttgactta-attgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
    ||  |  ||  ||| | || | ||  ||||  ||  ||      |||||  ||||||| | |||||  ||| |  | ||  || ||    ||  || |||||||| |||||||||||||||||| |  ||||||| ||||| |||||| |||| |||||
tatctacctcatcagtgattaatgtaaggagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM5G824831_T03 (Zea mays), 3'ss of exon 9
---ttatatt-tctttgaatgatttgagttgcattagttttacctcatttcat--tttccctatcatttc-tatggttgactta-attgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
    ||  |  ||  ||| | || | ||  ||||  ||  ||      |||||  ||||||| | |||||  ||| |  | ||  || ||    ||  || |||||||| |||||||||||||||||| |  ||||||| ||||| |||||| |||| |||||
tatctacctcatcagtgattaatgtaagcagcatgtgtgctataattgttcatcctttccctctgatttcacatgttatatttgtatggtttcattgtagATACACAGAAGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G085243_T01 (Zea mays), 3'ss of exon 9
---------ttatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
         ||| |   | ||             |||  ||      | || |||| || |   |     |  |||  ||    ||  | | || ||  || |||||||| |||||||||||||||||| |  ||||||| ||||| |||||| |||| |||||
gtgtaagatttagagcccattaccaccccctgtgtgccataacagatcatcctttccttctgatttcacatcttatatttataatatgttttca-ttgtagATACACAGAGGATATGGAGCTTGATGATGCCATCCACACTGCAATTTTGACTTTGAAAGAAGG

upper sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
lower sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 9
-ttatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
 | ||| |  |||  |  ||||| | || || |||||    || |   |     | | |||||||         |||| |  |  |    |||||||||||| |||||||| ||||||||| |  | ||||| |||||||||||  ||||||||||
gtgataataattt--accatttgtggtg-atgagtttatgatcttggaa----gcatgtcatttc-------atcttagtctttgat---cagGTACACAGAAGATATGGAACTTGATGATGCCATTCACACGGCAATATTGACATTGAAGGAAGG

upper sequence: GLYMA03G16660.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 8
--ttatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccactt------acaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
  ||   || |  |       ||   |  ||||   ||| | |    ||  |||     | | ||    ||   | |||||      |||        |||||||| ||||||||||| ||||||||| | ||||||||||| || ||||| || ||||| ||
ttttcctttcccattcccttcttttttaacattcaatttcctttccctctctttgatcttaacttaggaggagaatttaatatcttccttttccatgtagGTACACTGATGATATGGAACTTGATGATGCTGTCCACACAGCTATTTTGACACTCAAGGAGGG

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|151411475|gb|EV281286.1|EV281286
EST:     TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAG                         G
genomic: TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagat ... aggtacacag-
EST: gi|151411475|gb|EV281286.1|EV281286
EST:     TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAG                         G
genomic: TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagat ... aggtacacag-
EST: gi|151411475|gb|EV281286.1|EV281286
EST:     TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAG                         G
genomic: TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagat ... aggtacacag-
EST: gi|22933042|gb|BU550181.1|BU550181
EST:     TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGGTACACAG                  
genomic: TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAG-A-A-G-----AGgtaaatagat ... agg
EST: gi|12772361|gb|BG237288.1|BG237288
EST:     TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAG                         ATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGG
genomic: TCTGCTATGGGGAAAAATGTTTCTAATGCAAAGACTTTTCTTGAGAAGAGgtaaatagat ... aggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattttccctatcatttctatggttgacttaattgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG
                                      cacttac  putative branch site (score: 2)
          tatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatttctttgaatgatttgagttgcattagttttacctcatttcattttccctatcatttctatggttgacttaattgtccacttacaggtacacagATGATATGGAGCTTGATGATTCAGTCCACACAGCAATATTGACTCTGAAGGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - -tgatttg
- - - - - - - - - - - - -tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtccac