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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaatttgttcactaaaaaaatttgcttgctttataccccagtataacaaaaatcattaagcaaatgacttgacataatatatttgacggtaaatgttttatgtgtttctatttttttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTATGATATTGCAGAAGGTTGCTTATGCTACCGAGAGGGGGGTGATGGAGTAG

Basic information

species Glycine max
transcript GLYMA10G34220.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34220.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv13s0019g05360.t01 (Vitis vinifera), 3'ss of exon 9
gtaggaatttgttcactaaaaaaatttgcttgctttataccccagtataacaaaaatcattaagcaaatgacttgac---ataatatatttgacggtaaatgttttatgtgtttctatttt-----tttatta-cagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTATGATATTGCAGAAGGTTGCTTATGCTACCGAGAGGGGGGTGATGGAGTAG
                                   ||||        |  |  ||  |||| |        ||||     || || | || |    |  |||||||| ||  || | | ||     || | |  |||||||||||| || ||||| || ||||||||||| ||| |||| || || |||||| |||||||||| |||| |||| | |||||| |   |||    |  
----------------------------------gtataaaaagaacttcctgaagccatttaagttgctgcttggttggatgatttcttgggtaatggatgttttaagtaattttttgttgtaccttcactggcagGAAAGTTACAATCACAGGGTCACAGAGAGCAATCCGTGCAGCAGAGTCCATGATAATGCAGAAGGTAGCTTCTGCTTCTGAGAGGTGATGGATAAGTTTT
















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|193461496|gb|FK428895.1|FK428895
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|22927860|gb|BU544999.1|BU544999
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|193520218|gb|FK474667.1|FK474667
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|15202846|gb|BI425623.1|BI425623
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|6071922|gb|AW101309.1|AW101309
EST:     GAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: GAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|6502014|gb|AW203387.1|AW203387
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|192308183|gb|FK001281.1|FK001281
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|192303155|gb|FG997731.1|FG997731
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|193665257|gb|FK607969.1|FK607969
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|7590589|gb|AW706338.1|AW706338
EST:     TTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: TTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
EST: gi|24205232|gb|BU964485.1|BU964485
EST:     AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAG                         GAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT
genomic: AGGATAAAGATATCAGATAGAGGTGATTACGTATCTGGAACAACCGATAGgtaggaattt ... tttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacataatatatttgacggtaaatgttttatgtgtttctatttttttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTATGATATTGCAGAAGGTTGCTTATGCTACCGAGAGGGGGGTGATGGAGTAG
           atttgac  putative branch site (score: 4)
                                   tttctatttttttatt  putative PPT
                    taaatgttttatgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaatttgttcactaaaaaaatttgcttgctttataccccagtataacaaaaatcattaagcaaatgacttgacataatatatttgacggtaaatgttttatgtgtttctatttttttattacagGAAAGTTACCATAACAGGATCCCAGAGAGCAATACGTACAGCTGAATCTATGATATTGCAGAAGGTTGCTTATGCTACCGAGAGGGGGGTGATGGAGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA