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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...nnnnnnnnggttccccccccccccccccccccctccccatatggaatttattgctgctggaggggctgatcatttatggtattttgttcacaatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAAAGTTGAATTTGGCCTTCCTGATTTAGAGAGTAGGACTCAGATATTCAAG

Basic information

species Glycine max
transcript GLYMA03G42370.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 8
---------nnnnnnnnggttccccccccccccccccccccctccccatatggaatttattgctgctggaggggctgatcatttatggtattttgttcacaatttc-cagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAAAGTTGAATTTGGCCTTCCTGATTTAGAGAGTAGGACTCAGATATTCAAG
                 ||||       |            |||  |  |     ||   ||   ||       || |  |||||    |||| ||| |  ||||  |||||||||||| || |||||||||||  |||| |||||||| || ||||| || ||||| ||||||||||||||||| |||||||| || |||||||| |||
cataattctagatataaggtttgattttcaagtttttgggtctcttc-cactagcttagatgtctcta------cttacaatttaa---atttggtttatcattttacagGCCTGACACACTTGATCCAGCACTGTTACGCCCTGGACGGTTAGACCGCAAGGTTGAGTTTGGCCTTCCTGATTTGGAGAGTAGAACACAGATATTTAAG
















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|214009507|gb|DB988648.1|DB988648
EST:     GATGTGTAACATGCTCAAGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|16277955|gb|BI942651.1|BI942651
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGNACGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|208081456|gb|GD884336.1|GD884336
EST:     ATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: ATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGC-AACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|209718786|gb|BW671987.1|BW671987
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|37994041|gb|CF805787.1|CF805787
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCA-CACTACTACGACCTGGACGATTGGCCCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|213600067|gb|DB976026.1|DB976026
EST:     GAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTGCAACGACCTGGACGATTGGACCGTAA
genomic: GAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|209702900|gb|BW667435.1|BW667435
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|214007120|gb|DB986168.1|DB986168
EST:     GATGGGTTTGATGCTCGTCGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|193685395|gb|FK626611.1|FK626611
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGGATCCAGCACTACTACGACCTGGACGATTGGACCGTA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGG-ATCCAGCACTACTACGACCTGGACGATTGGACCGTA
EST: gi|193658883|gb|FK607300.1|FK607300
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|193429086|gb|FK396344.1|FK396344
EST:     CAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGATGATTGGACCGTAA
genomic: CAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|193682156|gb|FK621280.1|FK621280
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGATCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|193322175|gb|FK287053.1|FK287053
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGATCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|193350834|gb|FK314156.1|FK314156
EST:     TGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGATCGTAA
genomic: TGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|193386094|gb|FK352408.1|FK352408
EST:     CTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: CTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|21601986|gb|BQ612317.1|BQ612317
EST:     GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGTGGAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|214007458|gb|DB987315.1|DB987315
EST:     GAAACATCAAAGTCTTGATGGCAACTAACAG                         GCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: GAAACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
EST: gi|213611119|gb|DB974993.1|DB974993
EST:     AACATCAAAGTCTTGATGGCAACTAACAG                         GGCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA
genomic: AACATCAAAGTCTTGATGGCAACTAACAGgttttctgat ... caatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattgctgctggaggggctgatcatttatggtattttgttcacaatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAAAGTTGAATTTGGCCTTCCTGATTTAGAGAGTAGGACTCAGATATTCAAG
                  ggctgat  putative branch site (score: 4)
                                                tttcc  putative PPT
                          atttatggtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
nnnnnnnnggttccccccccccccccccccccctccccatatggaatttattgctgctggaggggctgatcatttatggtattttgttcacaatttccagGCCTGACACTCTGGATCCAGCACTACTACGACCTGGACGATTGGACCGTAAAGTTGAATTTGGCCTTCCTGATTTAGAGAGTAGGACTCAGATATTCAAG

- - - - - - ccccccc
- - - - - - - - - - - - - - - - - ccccata
- - - - - - - - - - - - - - - - - - - - - - - - - ttgctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagggg