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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgaaatttcttattgaatcaattttgaactacatcttgctgtattgtgtgtgattttgaatattcacgatgatgataattttttagtctttttctctccctttctctctggacacacacctacttgagacttgagagactggattacttgaaggaagaattttatatcttatctgtttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGCTGTGATGGAGGATATCCCTTATATGCATGGCGATACTTAG

Basic information

species Glycine max
transcript GLYMA03G38520.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtgaaatttcttattgaatcaattttgaactacatcttgctgtattgtgtgtgattttgaatattcacgatgatgataattttttagtctttttctctccctttctctctggacacacacctacttgagacttgagagactggattacttgaaggaagaattttatatcttatctgtttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGCTGTGATGGAGGATATCCCTTATATGCATGGCGATACTTAG
                                                                                                 | |||    ||   | || |     ||  |||||| ||||       |   ||||       |   || ||    | ||| ||||| |||||||||||| ||||||||||| ||||| ||  | ||||||||||||||| ||||||||  ||| |||||||| || |||||  | |||||||||||||| ||  
------------------------------------------------------------------------------------------------gtatcttgtatttgttatgaatg---acaaacttgacactt-------tttcttacg-attctagtcatattgatccctatatgttttattgcagAATATTTCTCTCTCTGTAAATGATCTCTTAGCATGCTGTGGCTTTTTGTGTGGAAGTGGTTGTGATGGGGGTTATCCTCTTTATGCATGGCGATATTTTA
















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|192323979|gb|FK015700.1|FK015700
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|192329589|gb|FK021903.1|FK021903
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|58018606|gb|CX705348.1|CX705348
EST:     TTGGTGCTGTTGAATCATGGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|151398613|gb|EV268484.1|EV268484
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAGTGACCTTCTTGCATGCTGCGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|19346536|gb|BM891416.1|BM891416
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|120532302|gb|EH260435.1|EH260435
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|151400974|gb|EV270788.1|EV270788
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|18713013|gb|BM522699.1|BM522699
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|192308925|gb|FK002149.1|FK002149
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|151411964|gb|EV281775.1|EV281775
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|8670417|gb|BE191524.1|BE191524
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|6666111|gb|AW277570.1|AW277570
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
EST: gi|10238899|gb|BE807795.1|BE807795
EST:     TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT                         AATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT
genomic: TTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTTgtaagtgaaa ... ttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagagactggattacttgaaggaagaattttatatcttatctgtttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGCTGTGATGGAGGATATCCCTTATATGCATGGCGATACTTAG
                                           gtttaat  putative branch site (score: 4)
                                        tctgttt  CT-rich tract
                       aagaattttatatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgaaatttcttattgaatcaattttgaactacatcttgctgtattgtgtgtgattttgaatattcacgatgatgataattttttagtctttttctctccctttctctctggacacacacctacttgagacttgagagactggattacttgaaggaagaattttatatcttatctgtttaattgcagAATATCTCTCTCTCTGTTAATGACCTTCTTGCATGCTGTGGCTTTCTGTGTGGATCTGGCTGTGATGGAGGATATCCCTTATATGCATGGCGATACTTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT