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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttagtcatatcactattcactattcttcttctatttttgtcaatttttttattttttttatttttgtgattgaaatttgggtatttggtttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGGTCTTTTGATGGGTGTGGATCTTGTGTTAAGATTCCTCAGGCTTCATCTG

Basic information

species Glycine max
transcript GLYMA11G19800.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19800.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G44880.1 (Arabidopsis thaliana), 3'ss of exon 1
ttttagtcatatcactattcactattcttcttctatttttgtcaatttttttattttttttatttttgtgattg---aaatttgggtatttggtttttg-gcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGGTCTTTTGATGGGTGTGGATCTTGTGTTAAGATTCCTCAGGCTTCATCTG
   |   || |      |  |||  |  |  | ||| |     || ||||    ||   | |||  |||| |||   |  | | | |   | ||  ||  | ||||||| ||| | |||||  ||||  | ||||| ||||| |||||||| ||||| |||| |||||||||||||||   || ||||||||||||| |  || 
--atgagcaaaaagaagtaaact--ttgttgtgtatgtaaccaaagttttgagcttgactcattgatgtgtttgtgtatgtgttgatgcattgtggttatgtagGAAGGAAGGTTGGATGAGAATGGACACTTGCAATGTTCGTATCATGGATGGTCATTTGGTGGGTGTGGATCTTGCACTAGGATTCCTCAGGCTGCTACTT
















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|4313516|gb|AI460635.1|AI460635
EST:     AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCT                         GAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
genomic: AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCTgtgagtatat ... tttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
EST: gi|213595843|gb|DB955963.1|DB955963
EST:     AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCT                         GAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
genomic: AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCTgtgagtatat ... tttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
EST: gi|254317552|gb|GR826536.1|GR826536
EST:     AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCT                         GAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
genomic: AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCTgtgagtatat ... tttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
EST: gi|11687706|gb|BF595382.1|BF595382
EST:     AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCT                         GAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
genomic: AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCTgtgagtatat ... tttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
EST: gi|209703485|gb|BW683346.1|BW683346
EST:     AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCT                         GAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG
genomic: AATGGGTTGCTTTTGATGACAAATGCCCCCATCGTCTTGCCCCTTTATCTgtgagtatat ... tttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttattttttttatttttgtgattgaaatttgggtatttggtttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGGTCTTTTGATGGGTGTGGATCTTGTGTTAAGATTCCTCAGGCTTCATCTG
                                             ttttt  CT-rich tract
     ttattttttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttagtcatatcactattcactattcttcttctatttttgtcaatttttttattttttttatttttgtgattgaaatttgggtatttggtttttggcagGAAGGGAGGATAGATGAAGATGGGAAGTTGCAGTGTTCTTATCATGGGTGGTCTTTTGATGGGTGTGGATCTTGTGTTAAGATTCCTCAGGCTTCATCTG

- - - -catatca
- - - - - - - ctattca
- - - - - - - - - - - - - cttcttc