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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtgttgtttccgtgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC

Basic information

species Glycine max
transcript GLYMA08G18240.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 3
ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtg-ttgtttccgtgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
   |    ||    || ||| ||| |  |   ||   | ||  | |    | ||  |||||    | |  |  | || ||  |||| ||    |||| |||||||| || ||||| |||||| ||||||||||||| || || |||||||| ||||| ||||| ||||| ||||| |||||||| ||   ||| ||| | |
-gttgttgaactgctcaatcgtttttagtatgtatgtacttcatatgcaatctgtttatttgttttatatagttctgatttcttccttgtgatttgtacagACTGTTCGCTTCAAGAATGAGCTGGAGCGTAACATCACTATAAAGCTTGGTTATGCTAATGCGAAAATCTACAAATGTGAAGACGAGAAATGCCCACGAC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 3
--ttatacataagcattccatcttttattcttaatacacattt-tcttttagctttggatatttacactgttgacctgtgttgtttccgtgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
  | ||  | |    |   || |  ||||  |  |   ||  | |  || |  | |  ||||||  |  |||| ||||  |   |||| ||  || | || |||| || || ||||| |||||| ||||||||||||| || || |||||||||||||| ||||| ||||| ||||| |||||||| ||   ||||||| | |
gttcatgaacatctttcatatttagtatttatgttcttcacatgtaattcatatatttatatttgtatagttgtcctg-atgtcttccttg--tgatttgtagACCGTTCGCTTCAAGAATGAGCTGGAGCGTAACATCACTATAAAGCTTGGCTATGCTAATGCGAAAATCTACAAATGTGAAGACGAGAAATGTCCACGAC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G117900_T01 (Zea mays), 3'ss of exon 3
ttatacataagcattccatcttttattcttaata----cacattttcttttagctttggatatt-tacactgttgacctgtgttgtttccgtgaa----tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
          | | |   | ||| | ||  |||       ||   | |||  |||| | || || |    | |  ||   | || |    |  ||    ||   || ||||||| || ||||| |||||| |||| ||||||||||| || ||||| |||||||| ||||||||||| ||||| ||||| |||||  |||||||| | |
---------ggaactttttttttgagtcccaatcatttttcaccatgtttgtgcttggtatgttatttgttttccacaaatattttgatggctaagttttgccttgtagACTGTTCGGTTCAAGAATGAGCTGGAACGTAACATTACTATAAAGCTGGGCTATGCTAATGCAAAAATCTACAAATGTGAGGATGACAGATGTCCACGAC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107654_T01 (Zea mays), 3'ss of exon 3
ttatacataagcattccatcttttattcttaatacacattttct---tttagctttggatatttacactgttgac-ctgtgttgtttccgtgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
    |  | |   || |  |  | | || |  | |||  | |||    || |  |   || | |    |  | |   | || ||  |   |    | | || ||||||| || ||||| |||||| |||| ||||||||||| || ||||| || || || ||||||||||| ||||| ||||| |||||  |||||||  | |
----aactgattttttcgaccctcaatcctttttcaccatgtctgtgcttggtatataatttgttttatactaatattttggtggcttaattttggctttgtagACTGTTCGGTTCAAGAATGAGCTGGAACGTAACATTACTATAAAGCTGGGTTACGCTAATGCAAAAATCTACAAATGTGAGGATGACAGATGTCCGCGAC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
-------ttatacataagcattccatcttt-tattcttaatacacatttt--cttttagctttggat-atttacactgt------tgacctgtgttgtttccgtgaatgtt--gtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
       ||    ||  |  || ||   || || || ||       || |  |||  ||| || ||| | ||  | ||       |||  | | | |||||| |   |  |  || |||||||| ||||| |||||||| ||||||||||||||||| || |||||||| |||||||| || || || ||||| ||||| |||||   ||| || || |
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: AT4G18330.1 (Arabidopsis thaliana), 3'ss of exon 2
-----ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtgt-tgtttccgtgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGG-CTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
     ||| || |  || ||    |   |  |||   |  | | | |   ||    |   | |    || |  ||  ||   | | | || |  |   |||  ||    |  |     |||  |    |  || | ||  |  |  |   | |  | || |||   |  || |||  |  || | | |     ||            
gtaaattacac-tctgc-ttttgccagctcctctaggtctatagtataacttgatgtcaaagaaac-caatactgtgctaaatatatctcagGAACCATTGGTCATGTCGCTCACGGTAAA--TCGACTATAGTGAAAGCTATCTCTGGTGTTCAGACTGTGCGT-TTTAAGAATGAATTAGAGCGTAACATTAC------------

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 3
ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtgttgtttccgtgaatgt-tgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
|||      ||    ||||  |  || ||  |   |  || |     |  | |  ||  ||| |      |  ||     ||    |   | | | | |||||||| ||||| ||||||||| ||||||| || ||||| ||||| ||||| |||||||||||||| |||||||| |||||||||||||| || ||  | |
ttaggagacagtggaccatagtc-atcctctagttattttgttaagaatatctatatgcttagatctgaaaggtggccctttatgatttgtttatctacagACTGTTCGTTTTAAAAATGAGCTGGAGCGAAATATTACTATCAAACTTGGATATGCAAATGCAAAGATATACAAATGTGAAGATGAACGGTGCCCTCGTC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 2
ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtgttgtttccg--tgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
 || |     |    ||||  |  || ||  |   || || |     |  |||  |   ||| |      |  || ||  |||  |  | | |  | | |||||||| ||||| ||||||||| ||||||| |||||||| ||||| ||||| ||||||||||| || |||||||| |||||||||||||| || ||  | |
-tagaagatggttgaccatagta-atcctctaattactttgttaaaaatatttacaggcttaaatctgaaaggtgggtcctttatggtttatttatctacagACTGTTCGTTTTAAAAATGAGCTGGAGCGCAACATTACTATCAAACTTGGATATGCAAATGCCAAGATATACAAATGTGAAGATGAACGGTGCCCTCGAC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 1
ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtgttgtttccgtgaa-tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
                      | ||    |       || | | |    |   ||  || |   ||||  | |   ||| |||  ||   || |   |||||||| || ||||| ||||| |||||||||||||| ||||||||||| |||||||| ||||| || || |||| ||||||||| || ||||| ||  |||
---------------------gtgatctagagcttgttttgtgtctccagtgccga-gttgatgttgttttctttgtttgattctttgttctgcttctcagACTGTCCGCTTCAAGAATGAATTGGAGCGTAACATCACAATCAAGCTCGGCTATGCGAATGCGAAGATTTACATGTGTGAAGACGAGCGATGCCCTCGGC

upper sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 1
ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtgttgtttccgtgaa-tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
                      | ||    |       || | | |    |   ||  || |   ||||  | |   ||| |||  ||   || |   |||||||| || ||||| ||||| |||||||||||||| ||||||||||| |||||||| ||||| || || |||| |||||||||||| ||||| ||  |||
---------------------gtgatctagagcttgttttgtgtctccagtgccgagtttgatgttgttttctttgtttgattctttgttctgcttctcagACTGTCCGCTTCAAGAATGAATTGGAGCGTAACATCACAATCAAGCTCGGCTATGCGAATGCGAAGATTTACATGTGTGAAGATGAGCGATGCCCTCGGC

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|19935170|gb|BQ080200.1|BQ080200
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|17023024|gb|BM094058.1|BM094058
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|17023965|gb|BM094999.1|BM094999
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|7478465|gb|AW666276.1|AW666276
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|209708854|gb|BW673890.1|BW673890
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|213606648|gb|DB959060.1|DB959060
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|23727056|gb|BU761544.1|BU761544
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|208219667|gb|GE016593.1|GE016593
EST:     ACGTGGCCCANGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|208147563|gb|GD945384.1|GD945384
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
EST: gi|15663764|gb|BI701135.1|BI701135
EST:     ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCA-GTGTCCAG                         ACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC
genomic: ACGTGGCCCATGGCAAGTCAACAGTTGTGAAAGCAATATCAGGTGTCCAGgtattccttt ... tgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagctttggatatttacactgttgacctgtgttgtttccgtgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
                    tgttgac  putative branch site (score: 3)
          atatttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatacataagcattccatcttttattcttaatacacattttcttttagctttggatatttacactgttgacctgtgttgtttccgtgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG