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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattggttttatttctaactctttatgacttggctatatttcatatttttgttttgttgcttctcttattttggttttgttgctttcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTAC

Basic information

species Glycine max
transcript GLYMA13G09970.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G031529_T01 (Zea mays), 3'ss of exon 10
gtattggttttatttctaactctttatgacttggctatatttcatatttttgttttgttgcttctcttattttggttttgttgctttcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTAC
          |||   | | | | | ||   |  |||| |   ||||        |  || ||     |||||   |||||   | |      ||||||||||||||| | || || || || |||||||| ||||| ||||| |||||||||||||||||   ||||||||||||   ||| ||||| ||| |||
---------gtatggattattgtatgtgctcttactatgt---atatcaggagcatactgttttatccatttt--ctttgtctgtctt-----tagGTGAAGAAGCATGTTAAGAAGGGCAAGAATGTTTCAATGGGATTTGGTTTTGTTGAGTTTGACTCTGTTGAAACTGCTACCGGTGTGTGCAAGGATCTAC

upper sequence: GLYMA13G09970.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0011g01060.t01 (Vitis vinifera), 3'ss of exon 11
gtattggttttatttctaactctttatgac-ttggctatatttcatatttttgttttgttgcttctcttattttggttttgttgctttcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTAC
      ||  | | | |  | ||||| ||| ||  | || | | || |       || |    |||    || || || ||     | ||     |||||||| |||| |||||||||||||| ||||| || ||||| ||||| ||| | |||||||| ||   ||| || ||    ||||||||||   ||||||
------gtaat-tcttttgcactttaggacctttcccatgtattatttgaccacattatg--ctcttacgttatgattctgacttgtccatgtgcagGTGAAGGAGCACTTGAAAAATGGGAAGAATGTGTCAATGGGTTTTGGTTTTATAGAGTTTGATTCAGTTGAGACAGCAGTCAATGTTTGCAGCAATTTAC
















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|254313854|gb|GR831483.1|GR831483
EST:     GGAAACATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCA-G                         GTGAAGA-GCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT
genomic: GGAAACATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAGgtattggttt ... tcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT
EST: gi|51334771|gb|CO978637.1|CO978637
EST:     GAACACATGAAAGAGGGAAGCANNNNGAGTGTCAAG                         GTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT
genomic: GAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAGgtattggttt ... tcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT
EST: gi|16348200|gb|BI973795.1|BI973795
EST:     GGAAACATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAG                         GTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT
genomic: GGAAACATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAGgtattggttt ... tcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT
EST: gi|10709774|gb|BF009498.1|BF009498
EST:     GGAAGCATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAG                         GTGAAGAAGCATTTGAAAAATGGGGAAAATGTTTCTATCGGGGCT-GGATT
genomic: GGAAACATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAGgtattggttt ... tcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTAT-GGGGTTTGGATT
EST: gi|15287874|gb|BI471765.1|BI471765
EST:     GGAAACATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAG                         GTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT
genomic: GGAAACATTTAACTGAACACATGAAAGAGGGAAGCATTTTGAGTGTCAAGgtattggttt ... tcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatatttttgttttgttgcttctcttattttggttttgttgctttcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTAC
                                       ttgctttc  CT-rich tract
     tttttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattggttttatttctaactctttatgacttggctatatttcatatttttgttttgttgcttctcttattttggttttgttgctttcacaaatagGTGAAGAAGCATTTGAAAAATGGGAAAAATGTTTCTATGGGGTTTGGATTTGTTGAGTTTGACTCCCCTGAAACTGCTACAAATGTTTGCAAAGATTTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG