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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttatgtgatggaatggttattttttatgatttgcagtttctttccagaaggatattttaacattagtacttgtctgattgtcctacttttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCTATTCGTCCTACTAGTGAAACTGTCATGTATCCCTACTACTCTAAGTGGA

Basic information

species Glycine max
transcript GLYMA03G38340.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 5
---gttttatgtgatggaatggttattttttatgatt--tgcagtttctttccagaaggatattttaacattagtacttgtctgattgtcctacttttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCTATTCGTCCTACTAGTGAAACTGTCATGTATCCCTACTACTCTAAGTGGA
   |||| |          || | ||||   |  | |  |     || |||    ||   ||| | | |  || || ||   || |  |  |   |||     |||| |||||||| ||||| |||||  |||| || || ||| | ||||||||||||||||| || ||||| ||||||||||||||||| || ||||||||||
attgtttaagaactcatggtgctcatttgacaaaaatgttatgaattattttattaatcctatctcacc--taatattt---tggtaatgttgactttttcctagGTCGCTTGGGTAACAAAATCTGGACAATCAGATTTGGAAGTGCCTATTGCTATTCGTCCAACAAGTGAGACTGTCATGTATCCCTATTATTCTAAGTGGA
















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|213588977|gb|DB971514.1|DB971514
EST:     CTAGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTG
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTG
EST: gi|213610669|gb|DB961144.1|DB961144
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|209724628|gb|BW677721.1|BW677721
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|193328627|gb|FK294003.1|FK294003
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|193510235|gb|FK470247.1|FK470247
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|192304983|gb|FG996115.1|FG996115
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTGACAAAGTCTGGAGAATCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|192330459|gb|FK022646.1|FK022646
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|207840337|gb|GD811356.1|GD811356
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTAAG                         GTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|19053180|gb|BM731847.1|BM731847
EST:     AGGAGAAGGACCACGTTGAGGGTTTTGCTCATGAG                         GTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
genomic: AGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT
EST: gi|193672000|gb|FK616298.1|FK616298
EST:     CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAG                         GTTGCTTGGGTGACAAAG-CTGGGGAGTCTGAATTAGAAATTCCTATTGCT
genomic: CTGGAGTTCTGCAAAAGGAGAAGGACCACGTTGAGGGTTTTGCTCCTGAGgtgagagttt ... tttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccagaaggatattttaacattagtacttgtctgattgtcctacttttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCTATTCGTCCTACTAGTGAAACTGTCATGTATCCCTACTACTCTAAGTGGA
                                   ttgtcctacttttcc  CT-rich tract
         atattttaacattagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttatgtgatggaatggttattttttatgatttgcagtttctttccagaaggatattttaacattagtacttgtctgattgtcctacttttccatcagGTTGCTTGGGTGACAAAGTCTGGGGAATCTGAATTAGAAATTCCTATTGCTATTCGTCCTACTAGTGAAACTGTCATGTATCCCTACTACTCTAAGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - -gtgatgg
- - - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg