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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA

Basic information

species Glycine max
transcript GLYMA11G07530.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g47600.1 (Oryza sativa), 3'ss of exon 6
tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctgcta-cagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA
  ||| | | |   || ||    | || |      ||| |||  | | | |   |       |||    |  |  ||      | ||  |  ||| | ||||||||||  ||||||||||||||||| |||||||||||||||||||| | |||||| | ||  |||||||||||  | || || || || |||   || |
agtcagtagcccaaca-caagaaagaaataatggtattctgtaccaagtgattatgatctaatggcttgagttcttacacatgatcatttgatgcaaacagGGTGAGAAAGATGACAAGATCATAGCTGTTTGTGCTGATGACCCTGAATACCGCCACTTCAGGGACATCAAGGAAATCCCCCCTCACCGCCTTCAAGAGA

upper sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G046587_T02 (Zea mays), 3'ss of exon 6
---tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA
    ||    | |  |  || ||   ||| |||   |||  | ||     |  || |   || | | |      ||| || |   |    ||     |||  ||| ||||  ||||| ||||| |||||||| ||||||||||||||||| ||||| || ||||| ||||||| ||| || || || ||||| |||   || |
gacctttctatagaatataatataatatagttcttgtaaactagttctgtcccaaggctgaattcttgcatcttatt-taatcgttgttcaacatcacta--gGGCGAGAAAGATGATAAGATTATAGCAGTCTGTGCTGATGACCCTGAATTCCGTCACTACACGGACATCACGGACCTCCCACCGCATCGCCTTCAAGAGA

upper sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 6
tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctg----ctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA
           |  ||| |   | |||  |    |||| |  | | |  ||| |||  |  || |  | |||  |    |   | |   |||||     | ||||||||||  || ||||||||||| ||||| ||||||||||| || |||||||| || |||| ||||||||| |||||||| || || || || |||||||
----------gtaacaaaaactcttaaacc---caattctacctctatgtaatgtattaccttagtaagaaaccaggaatc--accttgttctgaaacttgcagGGTGAGAAAGACGACAAGATCATTGCAGTATGTGCTGATGATCCCGAGTTCCGTCACTACAGAGACATCAAAGAGCTTCCCCCTCACCGTCTAGCTGAAA

upper sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 5
tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattat-attttcta-acaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA
  || ||     || || |||  |    |    |  |  |   |    | ||   || | ||   ||    ||||  |  |  || |||||| ||  | |||||||| | ||||||||| || |||||||| |||||||||||||||||||||||||| |||| ||||||||| ||| |||| |||||||| |||||||| |
agtctctatatatttaa-attagacgtgttttttcttgatcatatgtttcaagacacca-ttgaaagtgtgattaccaggtgatacacaaatccttttgcagGGTGAAAAGGATGACAAAATAATAGCAGTGTGTGCTGATGACCCTGAGTTCCGCCACTACAAAGACATCAAAGAGATTCCCCCACATCGCCTTGCTGAGA

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|33390382|gb|CA853577.1|CA853577
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAG
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAG
EST: gi|12689521|gb|BG155857.1|BG155857
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|10235681|gb|BE804569.1|BE804569
EST:     GTTCCTTACTTCGTGCTCGGGCTGTTGGACTAATGCCTATGATAGACCAA                         GGTGAGATGGATGACATGATC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATC
EST: gi|192316515|gb|FK009312.1|FK009312
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|17022265|gb|BM093299.1|BM093299
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|15661703|gb|BI699074.1|BI699074
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|11273956|gb|BF324342.1|BF324342
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATA
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATA
EST: gi|19452855|gb|BM954265.1|BM954265
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|192333273|gb|FK026154.1|FK026154
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|15814337|gb|BI786612.1|BI786612
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|193495770|gb|FK461108.1|FK461108
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|6481455|gb|AW200726.1|AW200726
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         NGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC
EST: gi|15203687|gb|BI426455.1|BI426455
EST:     GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAG                         GGTGAGAGGGATGACAAGATCATAGCAGCTTGTGCTGATGACCCTGAGTTC
genomic: GTTCCTTCCTTCGTGCTCGTGCTATTGGACTAATGCCTATGATTGACCAGgtaaaagttc ... tctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttaaagtacaaatttggagaaaaattatattttctaacaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA
                                  ttctaac  putative branch site (score: 1)
                                            ttctgct  putative PPT
            aaatttggagaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcacttggctttcaacattgcataattcgaataattttgtcaccacttaaagtacaaatttggagaaaaattatattttctaacaaattctgctacagGGTGAGAGGGATGACAAGATCATAGCAGTTTGTGCTGATGACCCTGAGTTCCGCCATTACACAGACATCAAGGAGCTTCCTCCACATCGGCTTGCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT