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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACAAGGGCTGCGTCGGTGCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctatcaactggccctctttttcccatatccactgttatatttcatgttattaccatttctgctgtctttacttcccagcaatgtcactctatagatgagtaacaccttttgactaatttgaagtttagtctgaatgtttgttcattaaaactgttactgttttag

Basic information

species Glycine max
transcript GLYMA02G45610.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G45610.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv02s0025g01350.t01 (Vitis vinifera), 5'ss of exon 11
GCACAAGGGCTGCGTCGGTGCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctatcaactggccctctttttcccatatccactgttatatttcatgttattaccatttctgctgtctttacttcccagcaatgtcactctatagatgagtaacaccttttgact--aatttgaagtttag--tctgaatgtttgttcattaaa----actg---ttactgttttag------
|||||||| || ||  ||||  ||||||||||||||||||  | |||||| || ||||| |||||||||||||||    ||| |    | ||| |   || ||    | |||    |   ||    |   |   ||  ||  | | |        |   ||  | || |||     |  | ||  ||||  | |   |  ||  |  |||| || ||||| || |||     ||||   || ||||||  |      
GCACAAGGTCTTCGCAGGTGTGTTGAAGAGATTGTGTTCTCTTATACCTACCCTAGGCTTGATATGGAGgtttgt---acaatttctgcccttctcaacaaattttttcttaccacttgagta--cattgtccttggggtaatcaatcggtccagagtccagacaatggatacaatattctttgggactcaagtacaacattctgcatctggat-tttgtgcactaactcacactgacctttctgtttgtgcttcag
















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|208220404|gb|GE019836.1|GE019836
EST:     GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAG                         GTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
genomic: GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
EST: gi|193359948|gb|FK326720.1|FK326720
EST:     CATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTTAGATATGGAG                         GTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
genomic: CATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGC-TAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
EST: gi|298181814|gb|HO025989.1|HO025989
EST:     GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAG                         GTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
genomic: GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
EST: gi|208179591|gb|GD973594.1|GD973594
EST:     GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAG                         GTTTCTAAACATATGAATCATTTGCTTAAAGC
genomic: GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGC
EST: gi|151404405|gb|EV274215.1|EV274215
EST:     GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAG                         GTTTCTAAACATATGCATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
genomic: GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
EST: gi|58023254|gb|CX709995.1|CX709995
EST:     GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAG                         GTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
genomic: GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTTTGTGTACATCCT
EST: gi|19271087|gb|BM887343.1|BM887343
EST:     GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAG                         GTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTT
genomic: GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATATGAATCATTTGCTTAAAGCACCATTT
EST: gi|207792263|gb|GD764169.1|GD764169
EST:     GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAG                         GTTTCTAAACATA
genomic: GCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctat ... actgttttagGTTTCTAAACATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACAAGGGCTGCGTCGGTGCATTGAAGAGATTGTGTTCTGCTTTACCTATCCCAGGCTAGATATGGAGgtttgtctatcaactggccctctttttcccatatccactgttatatttcatgttattaccatttctgctgtctttacttcccagcaatgtcactctatagatgagtaacaccttttgactaatttgaagtttagtctgaatgtttgttcattaaaactgttactgttttag

- - - - - - - - - - - TTGAAG
- - - - - - - - - - -  TGAAGA
- - - - - - - - - - - -  AAGAGA