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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttctgattattttctttgttgttactgctatgtctgccttagaaatatattaaatctgtttagctccaatgcctagtgttatagttctgtcac...

Basic information

species Glycine max
transcript GLYMA19G41420.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41420.2 (Glycine max), 5'ss of exon 9
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 5'ss of exon 9
CCCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttctgattattttctttgttgttactgctatgtctgccttagaaatatattaaatctgtttagctccaatgcctagtgttatagttctgtcac---
||  |||| || || ||||||||||| ||||||||||||||||| |||||||||| ||   |  |  ||   |   |  |      |||  || |  | | | || |||||||   | |      | ||   | |     |  |  ||      
CCTCTGTTTCCTGGAGAGAGTGGAGTCGATCAGCTTGTTGAGATTATCAAGgtaa-ctacattgtatttcagtacatcatgcaaaatatagct-cgattgcattaaattaaatacatcttttctgagtgga-attaccggatctaggtgggagg
















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|58018658|gb|CX705400.1|CX705400
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
EST: gi|26047711|gb|CA784420.1|CA784420
EST:     CCTTGTTCCCTGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
EST: gi|9985319|gb|BE659427.1|BE659427
EST:     NNNTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
EST: gi|58024722|gb|CX711463.1|CX711463
EST:     TTGTTCCCCCGGTGAGAGTGGAGTTGATCAGCTTG-TGNAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: TTGTT-CCCCGGTGAGAGTGGAGTTGATCAGCTTGTTG-AGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
EST: gi|193407080|gb|FK375255.1|FK375255
EST:     CTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCATCAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: CTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
EST: gi|254328747|gb|GR833119.1|GR833119
EST:     TGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: TGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
EST: gi|193616610|gb|FK568242.1|FK568242
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
EST: gi|6963904|gb|AW432597.1|AW432597
EST:     CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAG                         GTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT
genomic: CCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttc ... gctttggtagGTTCTGGGAACTCCAACAAGGGAAGAGATAAAGTGCATGAATCCTAACTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTTGTTCCCCGGTGAGAGTGGAGTTGATCAGCTTGTTGAGATCATCAAGgtaatctttctgattattttctttgttgttactgctatgtctgccttagaaatatattaaatctgtttagctccaatgcctagtgttatagttctgtcac

- - - - - - - - - AGTGGA
- - - - - - - - -  GTGGAG
- - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - AGATCA