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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT

Basic information

species Glycine max
transcript GLYMA03G32800.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                    |  || |||   |   ||||   ||      |||||| | |  ||| | || |||  |    |    ||     | || |||    ||  | |  | | ||      | | ||  |  |  | | ||||   | ||  ||||||||||| || || |||||||| |||||||||||||| || |||||||||||||| || ||| | ||||||||||||||||| ||||| || ||||||
-------------------gtagagtagtgcatacttcaa---atgggaagtcttctatatgatgaatgttgtttgtgtatagtaaaagattg-gtggaacttcccatgaaatagt-ttata---tgagtattgatgaacttttttttttctccttatagGTATGATGCTCATTCGGGTGGAGAGCGTGAAATTCAGAGAACCATGTTGGAGTTGCTTAATCAGCTGGATGGTTTTGATTCAAGGGGAGATGTTAAAGTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggat-caattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                   ||||    || | |  |    |||    ||      |   | ||| | |  | || |||  ||| |  ||  ||   | | ||  | | | || |  |      ||| ||||||||||| || |||||||| || ||||| |||||||| || |||||||||||| | || ||| | ||||||||||||||||||||||| || ||||||
-------------------------------------------------ggtctttcccttcccggctgagatttttatgaaaa---aaatgttgctgaa--gcttctag--tgaaaggattaatatgagttttgctgtttctcgccct-----gttgtagGTATGATGCTCATTCTGGTGGTGAGCGTGAGATTCAGAGAACCATGTTGGAGTTGTTAAATCAGCTGGATGGTTTTGATTCAAGAGGAGATGTTAAAGTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G20140.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgattt---ttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                   | | | |   |   |  |     |  |||         ||  |     |    || | |     || ||||       |||   |  ||||      |  | || |   ||||||||| ||  |||| ||||| ||||||||||| || || || ||||||||  | ||||||||| | ||||| ||||||||||||||||| || || |||
--------------------------------------------------gtatgcctaaatacaacataaacatgatccattgataaacaatgttcttgattttgctcaagagatggtatc------taatatgtgatataaaatggtggt-tgaa--acagGTATGACGCAAACTCAGGTGGGGAACGTGAAATCCAAAGAACCATGTTGGAACTACTGAACCAGCTTGATGGGTTTGATTCAAGAGGAGATGTTAAGGTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagg-gggcaggggatgcgggactggt-tatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                                             |  ||     |             ||| | ||||      |   |  | | |  ||| | ||  |||   ||  | | |   ||||||||| || ||||| || || |||||||| || || || |||||||||||  | ||||||||| | ||||| ||||||||||||||||| || || || 
-----------------------------------------------------------------------------gtaagttaaactattttcataaacctgatctataacccattgataatggtta--tctgattacttgttgtttgaaagaa---cagGTATGACGCTCACTCAGGAGGTGAACGTGAGATCCAAAGAACTATGTTGGAACTTCTGAACCAGCTTGATGGATTTGATTCAAGAGGAGATGTTAAGGTC

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcat---ggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                                                 | | |  |  ||  |   | || | | | | | ||||  |    | ||  || ||  | ||  | ||   ||| | ||||||||||||||| ||||| ||||| ||||||||||| |||||||| ||||||||  |||| ||||||||||| |||||||||||||| ||||| || ||||| 
---------------------------------------------------------------------------------gtgagtcgatga-acattagtgatga-aaaatcatatttttcaagttcttttttttttttaattatcaaatattccttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatag-agtgatatcatggatcaa--ttcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                          ||||| ||  |    ||     | |   |      |        ||  | || | |  | ||   | | ||  || ||| |  |  | |  ||  |  |||  || || ||||| ||||| ||||||||||| ||||||||| ||||||||||||||||| |||| ||||| ||||| |||||| |  | || ||||||||||| 
----------------------------------------------------------ttttcagacgtagcatt----aaagtttcgaccagtctctagtgggccacagtattcgtttcgacgcttaagtttgttaatgaaaatttggttc-tttattatagATACGATGCTCACTCCGGTGGAGAACGAGAAATTCAGCGGACTATGTTGGAGTTGTTGAATCAGTTGGATGGATTTGATGCTCGTGGTGACGTAAAAGTC

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                          ||    |     ||  |  |              ||    ||||| || |    ||||   ||   | || |   |      ||   |  | |  | ||||| ||||||||||| || |||||||| || |||||||| ||||||||||||||||||||||| ||||| |||||||||||| |  | || || || || |||
---------------------------------------------------------gttgaaagccgacttaatatgtacatatttcaaatatttaagactg-ttttgtcatgatcaaatatttgaaattgaaagcggagttggtgcttt--actgcagATATGATGCCCATTCCGGTGGAGAGCGAGAAATTCAAAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGTTTTGATGCTCGTGGTGATGTTAAGGTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                |    |    |  | || ||| |  ||| |      | ||     |           | |  ||| || |  |    | ||||| |  ||     |   |  | |||||||| |||||||| || || ||||| ||| | || ||||||||||||||||||||||||||||| ||||| ||||| ||||||||  | ||||| || || |||
----------------------------------------------agcggcgtgtcgtggtttggtttatagttctgattacagtcataaatt----------ctgtctagtaatcttgt----ctattctgaaaattaacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ20767 (Selaginella moellendorffii), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                                                                 |   | |||  |  ||  |  ||   |  ||||    |   |   |  | | |        ||||||||||| |||||||||||||| || ||||||||| |||| ||| | ||| ||||||||||| | |||||||| ||| |  | || ||||| ||||||
-----------------------------------------------------------------------------------------------gtgatttcgttgcatggttgttgcagaaactaatt----gggaacaaccttctca--------agGTATGATGCACACTCTGGTGGAGAGCGCGAAATTCAGCGGACCATGCTTGAGCTGCTGAACCAGCTCGATGGTTTCGATGCTCGGGGTGACGTGAAAGTT

upper sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ32659 (Selaginella moellendorffii), 3'ss of exon 3
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                                                                                 |   | |||| |  ||  |  ||   |  ||||   |  |    |||||            ||||||||||| |||||||||||||| || ||||||||| |||| ||| | ||| ||||||||||| | |||||||| ||| |  | || ||||| ||||||
-----------------------------------------------------------------------------------------------gtgatttcgttacatggttgttgcagaaactaattgggaacaaccttctct------------agGTATGATGCACACTCTGGTGGAGAGCGCGAAATTCAGCGGACCATGCTTGAGCTGCTGAACCAGCTCGATGGTTTCGATGCTCGGGGTGACGTGAAAGTT

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|192327496|gb|FK019623.1|FK019623
EST:     TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAG                         GTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
genomic: TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAGgtaagttatt ... tgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
EST: gi|6725713|gb|AW310112.1|AW310112
EST:     TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAG                         GTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTCGGA
genomic: TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAGgtaagttatt ... tgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
EST: gi|58019738|gb|CX706480.1|CX706480
EST:     TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAG                         GTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
genomic: TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAGgtaagttatt ... tgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
EST: gi|208210474|gb|GE015637.1|GE015637
EST:     TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTAGTACTAAGAG                         GTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
genomic: TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAGgtaagttatt ... tgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
EST: gi|16996954|gb|BM086326.1|BM086326
EST:     TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAG                         GTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
genomic: TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAGgtaagttatt ... tgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
EST: gi|151412684|gb|EV282496.1|EV282496
EST:     TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAG                         GTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
genomic: TCCCCATCTATTGTCTTCATTGATGAGATAGACGCTGTTGGTACTAAGAGgtaagttatt ... tgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
EST: gi|254329469|gb|GR839032.1|GR839032
EST:     GCTGTTGGTACTAAGAG                         GTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA
genomic: GCTGTTGGTACTAAGAGgtaagttatt ... tgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT
                                    tctcttttat  CT-rich tract
                     aattcttagtatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA