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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcatttatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatttaaggagtgttccagcatcttaagacaatgccttttgtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT

Basic information

species Glycine max
transcript GLYMA10G04920.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 2
gtttgcatttatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatttaaggagtgttccagcatcttaagacaatgccttttgtgtatt-cagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT
                                      |    |||  |||| |  ||   |        || |   |  | | | | | | ||     |  |  |  ||      | |     || |   |||| ||||| || || || || |||||||||||||| ||||| |||||||| ||||| ||||| ||||||||| | || |||||||| || ||||| |||||| | |
------------------------------------gttcatatttttgcatatgattaaaaaggtgcaaattt---gatattatatagctatattttttccttgaaaattcatgaatatctttttgtaattattgcagGCGGTTGCTAATTCTACATCAGCAACATTTTTGCGTGTTGTTGGGAGTGAGTTGATCCAAAAGTACCTTGGTGATGGCCCCAAGCTTGTAAGAGAATTGT

upper sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------gtttgcatttatctttgcttcttc-tagagctgtt------ttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgattt---aaggagtgttccagcatcttaagacaatgccttttgtgtatt-cagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT
                                             |  |  | || | |||| |  ||  || ||| ||        | |  |  |||||   |    || || ||  | | |  | |   |  ||  || |||    ||    | ||  |    ||||| ||      |||||     |  |||| || || || || || |||||||| |||||||| |||||||| ||||||||||| ||||||||| | || ||||| || || ||||| |||||| | |
gtttgtgctgattccttgaggacagttccaagtttttatttccatgcct-tagttgtttttgttcattgataaagcagtgaaggaactgaacgcttttcattcttcttttcttcctgacataagatattctctatgcctttattcctaaaatcatattttaattacttaaaac------ttttgaacgctgtagGCTGTTGCCAATTCTACTTCAGCAACGTTCTTGCGTGTTGTTGGGAGTGAATTGATCCAAAAGTACCTTGGTGATGGTCCCAAGCTTGTTAGAGAATTGT

upper sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 2
--------------------gtttgcatt-tatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatct---ttaggcagtgttttgatttaaggagtgttc---cagcatct--taagacaatgcct-tttg----tgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT
                    || | ||   | ||  |   |    |||   ||       || | ||    |||| | |||  |||  ||||||    |||  |  | |||  | ||    ||| |||    ||||| |  |  |  | ||  |  |||    ||| | ||||| ||||| ||||||||||| || || |||||||| ||||||||||||||| | || ||||||||| | || ||||| || ||||| ||  ||||| | |
gtcagtattctgtcttgcaagtatacaagatgtcaatatattgcttagtattgcaggggcag-gctttgatatctgcctttgtctatgtttatccaaattacactctttttctacttttc-agttttcaaatagcatgtacttgggtagtgattacttgaaactgtctgcagGCTGTGGCTAACTCAACATCTGCGACTTTCTTGCGTGTTGTTGGTAGTGAACTCATTCAAAAGTACCTTGGGGATGGTCCCAAACTAGTCCGAGAATTGT

upper sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgcatttatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatttaaggagtgttccagcatcttaagacaatgccttttgtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT
                             ||   ||  | |  | ||    || |     |   |   ||    || ||  |||||   || ||| | |  |   |||    |||    ||     || |   || |||| || || || ||||||||||| || |||||| | ||||||||||||||  |||| || ||||| ||||||||||| || || ||||||||||||||||
--------------------------tgtcttcctttctcgtttctctctgtcacaagcatgagatagttgcaatttggtggtgtt---atctaatgggaat--aagctctctaacttgat----cttat---tttagGCGGTTGCGAATTCAACATCAGCTACTTTCTTGAGAGTTGTTGGTAGTGAGCTGATTCAGAAGTATTTGGGAGATGGTCCTAAGCTTGTGAGAGAACTTT

upper sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 2
gtttgcatttatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatttaaggagtgttccagcatcttaagacaatgccttttgtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT
                                || | ||  | |||    || | ||| ||  ||  |  |  |    | ||  |  |  |  |||   ||||| |  | |||   ||  |  | ||| |||| |||||| || |||||||| ||||||||||| ||||| || |||||||| ||||| || || ||||| || ||||||||||| |||||| | ||||| ||  | |
------------------------------ctttgttatttacttttcttatattcttgtt--tagttgaagatcagagtagcttccttgtcaaag--ttgttcta--aacttgcaaccct--catttatgtactcagGCAGTTGCAAACTCTACATCAGCAACTTTCTTACGTGTTGTTGGCAGTGAGTTAATTCAAAAATATTTGGGAGATGGGCCAAAATTAGTGAGGGAGTTAT

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|12772670|gb|BG237524.1|BG237524
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|192324369|gb|FK015720.1|FK015720
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGCGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|14991505|gb|BI317178.1|BI317178
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|23057351|gb|BU578025.1|BU578025
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|13480000|gb|BG509343.1|BG509343
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|193356897|gb|FK319589.1|FK319589
EST:     GGTCATTTTATTCTGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGTCATTTTA-TATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|17400370|gb|BM177152.1|BM177152
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|193381783|gb|FK346604.1|FK346604
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|193331048|gb|FK295364.1|FK295364
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|207822926|gb|GD794385.1|GD794385
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|254313973|gb|GR831602.1|GR831602
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         -CCGTG-CAAACTCAACATCAGCAACATTCTTGCGCGTTGT-GGTAGTGA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGA
EST: gi|207825707|gb|GD797334.1|GD797334
EST:     TCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: TCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|207821859|gb|GD794298.1|GD794298
EST:     GGGTCATTTTATATGGAGAACCTGGTACT-GGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|6454899|gb|AW185509.1|AW185509
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|208157920|gb|GD955573.1|GD955573
EST:     TCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: TCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|254316118|gb|GR825927.1|GR825927
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|208165264|gb|GD964428.1|GD964428
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|208265273|gb|GE061793.1|GE061793
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|298164759|gb|HO014404.1|HO014404
EST:     GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GGGTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|193406511|gb|FK371816.1|FK371816
EST:     GTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: GTCATTTTATATGGAGAACCTGGTACTGGGAAGACCTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
EST: gi|14011173|gb|BG726104.1|BG726104
EST:     CTTGCTTGCGAAG                         GCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA
genomic: CTTGCTTGCGAAGgtttgcattt ... gtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgatttaaggagtgttccagcatcttaagacaatgccttttgtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT
 ttttgat  putative branch site (score: 4)
                                       ccttttgt  putative PPT
      atttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcatttatctttgcttcttctagagctgttttaatagagtttcagcatctcctttttactacctttatctttaggcagtgttttgatttaaggagtgttccagcatcttaagacaatgccttttgtgtattcagGCCGTGGCAAACTCAACATCAGCAACATTCTTGCGCGTTGTTGGTAGTGAATTGATACAAAAGTACTTGGGAGATGGCCCAAAACTTGTGAGAGAACTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG