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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctctctctcggtttttttttttttcgcaatacctttaaaaaagttttattttttcatgtacccatttgttcactgcatgaaaatttgtttttttttccgcccatttggtgtgaatgtcgtatttttcgcttttaatgttggagggtattgttaaaattgttaattgatgcagttctgttgcatgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAGAGCAAAATCGTTTGGTGCTTCAGGGACCCAAGT

Basic information

species Glycine max
transcript GLYMA04G39390.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39390.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g00550.t01 (Vitis vinifera), 3'ss of exon 1
gtactctctctctcggtttttttttttttcgcaatacctttaaaaaagttttattttttcatgtacccatttgttcactgcatgaaaatttgtttttttttccgcccatttggtgtgaatgtcgtatttttcgcttttaatgttggagggtattgttaaaattgttaattgatgcagttctgttgcatgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAGAGCAAAATCGTTTGGTGCTTCAGGGACCCAAGT
                                                                                     | ||    || ||||||             |   |  || ||| ||   |||  |          | | |||  ||||| || |        || ||||| |  |    |||||   || || || || ||||| |  || |||||||||||||| ||||||||||| ||| | ||||  ||||| || |||||||||||||| || |||||
-------------------------------------------------------------------------------------agatcaccttatttttcaattttcactccctttctaacgcattatt--gtttagaaacatacatatgtagtttgaattgatagtct------ttttgttgaacct----tagGTTTGGGTGAAAGACCCTGGAAAACATCCGATGCTAGACTTGTTCTTGAAGATGGCTCAGTCTGGAAGGCAAAGTCATTTGGTGCTTCAGGAACTCAAGT
















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|298163265|gb|HO011998.1|HO011998
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|213620406|gb|DB957303.1|DB957303
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|298180620|gb|HO025707.1|HO025707
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|16997114|gb|BM086486.1|BM086486
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|298166083|gb|HO009054.1|HO009054
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|120531240|gb|EH259373.1|EH259373
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|207686059|gb|GD670385.1|GD670385
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|213605660|gb|DB972308.1|DB972308
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|192322448|gb|FK014929.1|FK014929
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|18735504|gb|BM528801.1|BM528801
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|209726906|gb|BW680261.1|BW680261
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
EST: gi|192326456|gb|FK017713.1|FK017713
EST:     ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGG                         GTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG
genomic: ACATGCTGCCGCCAAAGTTTCCGTCTTTACCGTCAGATGCTCTTCTTCGGgtactctctc ... tgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggagggtattgttaaaattgttaattgatgcagttctgttgcatgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAGAGCAAAATCGTTTGGTGCTTCAGGGACCCAAGT
        tattgttaaaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactctctctctcggtttttttttttttcgcaatacctttaaaaaagttttattttttcatgtacccatttgttcactgcatgaaaatttgtttttttttccgcccatttggtgtgaatgtcgtatttttcgcttttaatgttggagggtattgttaaaattgttaattgatgcagttctgttgcatgtgacatagGTAGTGGAGAGAGGCCTTGGAAGAATTCAGATGCTAGACTTGTGCTTGAAGATGGTTCAATTTGGAGAGCAAAATCGTTTGGTGCTTCAGGGACCCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA