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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaaacggttgcacccacaaaataataataaaaggttactagaaaattacagtgtattctgaaaatgtcttcctgagtccttttaatgtttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG

Basic information

species Glycine max
transcript GLYMA08G46570.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46570.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G25040.1 (Arabidopsis thaliana), 3'ss of exon 4
---actaaacggttgcacccacaaaataataataaaaggttactagaaaattacagtgtattctgaaaatgtc-ttcctgagtccttttaatgtttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG
   | | | |  ||  |  ||  | |||     | ||   |  |      ||      |||||   |  || | || |  |    ||| | |    |  ||||||||||||  | ||  ||||||||||||| |||||||| || ||||||||||| ||||||| |||
taaatttagcatttagattcaatagata----cataaatcttgtgttgtcttgattattattcgtcagctgacatttcaaaaatgtttgattacaatgatgcagCATGGATCGCCGGGTTTGTTCAAACACTGCTCTATGCCGACTTCTTCTATTATTATTTCCTAAG

upper sequence: GLYMA08G46570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0029g00180.t01 (Vitis vinifera), 3'ss of exon 5
--------------------actaaacggttgcacccacaaa-ataataataaaaggttactagaaaattacagtgtattctgaaa-atgtc-----ttcctgagtccttttaatgtttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG
                          |  |  | | || |   |||   ||  |  |  |     | |||   || | |  | |   |||||      || |   | |  | | | |  ||||||||| ||||| || || |||||||||||| | || |||||||||||||||||||| |||||||| ||
gtatgactctctctctctctctctctctctctctctcatatgcatatgtatgcacaggcatgcacatattcatgtctttaatcatgcatgtcaacacctcatttatgcaataattctacttttgcagCTTGGATATCAGGGCTTGTTCAAACATTGCTTTATGCTGATTTCTTCTATTATTATTTCCATAG
















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|192306206|gb|FG996834.1|FG996834
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAA-CACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|6566143|gb|AW233782.1|AW233782
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|209715073|gb|BW677116.1|BW677116
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|193314107|gb|FK281742.1|FK281742
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|9564202|gb|BE473711.1|BE473711
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|31305448|gb|CD390651.1|CD390651
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|10252890|gb|BE820656.1|BE820656
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|192325724|gb|FK015081.1|FK015081
EST:     CAACTGGATCTATCGCTACTTTACTGAGCTCCACTTTGTCCATTGGA-AA                         CATGGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTAT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGG-ATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTAT
EST: gi|21601718|gb|BQ612049.1|BQ612049
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|192306207|gb|FG996835.1|FG996835
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|27424798|gb|CA936318.1|CA936318
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|208059246|gb|GD859474.1|GD859474
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATG
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATG
EST: gi|208113393|gb|GD911578.1|GD911578
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|7147282|gb|AW509204.1|AW509204
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCACACTTTGTCCATTGGATAA                         CATGGATGTCTGGCCTTGGTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|8401987|gb|BE057621.1|BE057621
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
EST: gi|193612727|gb|FK560462.1|FK560462
EST:     CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAA                         CATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT
genomic: CAACTGGATCTATCGCTACTTTACTGAGCCCCACTTTGTCCATTGGATAAgtatgattct ... ttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacagtgtattctgaaaatgtcttcctgagtccttttaatgtttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG
                                    ttttaat  putative branch site (score: 3)
                                          tgttttttt  CT-rich tract
                                    ttttaatgttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaaacggttgcacccacaaaataataataaaaggttactagaaaattacagtgtattctgaaaatgtcttcctgagtccttttaatgtttttttgcagCATGGATTTCTGGCCTTGTTCAAACACTACTCTATGCTGATTTCTTCTATTACTATTTCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - cacccac
- - - - - - - - - -aaaataa
- - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - tacagtg