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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcctatcatcatgaagctttgctctataatatcatattaatttgcttagagtagagttaattgattgttgacctattacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGTCCCAACTACCAGAAGGGTCTAGCAAAAATGAGGGCACTCGGAGAGGAAA

Basic information

species Glycine max
transcript GLYMA15G42140.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G42140.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 12
gtgagcctatcatcatg-aagctttgctctataat-atcatattaatttgcttagagtagagttaattgattgttgacctattaca-aaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGTCCCAACTACCAGAAGGGTCTAGCAAAAATGAGGGCACTCGGAGAGGAAA
|||| | |||    ||   ||||||||   ||    ||  |   | ||| |||  |  |     | |  |||  ||   ||||    || ||||||  |||||| ||||   |||  |||||||| || || |||||||||||||| || ||||||| |||||| ||||||||| || | || ||||||||||
gtgatcttattcctattcgagctttgcaaaattcccatgttgccattttactttaaaaaataacactgaatttatgtattattgtgtaagcagGAATCAAAGCTTAAAGCTTCAAGAATGCACATATACGTTAGGAGAGGAGGTCCAAATTACCAGAGGGGTCTTGCAAAAATGCGGACTCTTGGAGAGGAAA
















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|14991230|gb|BI316903.1|BI316903
EST:     CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAG                         GAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctat ... tacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
EST: gi|7924163|gb|AW830189.1|AW830189
EST:     CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAG                         GAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctat ... tacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
EST: gi|6502280|gb|AW203653.1|AW203653
EST:     CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAG                         GAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctat ... tacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
EST: gi|6726078|gb|AW310477.1|AW310477
EST:     CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAG                         GAACAANAGCTAAAAGAAGCANAGATGCACATCTATGTGAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctat ... tacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
EST: gi|58022555|gb|CX709296.1|CX709296
EST:     CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAG                         GAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctat ... tacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
EST: gi|192330363|gb|FK021164.1|FK021164
EST:     CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAG                         GAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctat ... tacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
EST: gi|10253168|gb|BE820934.1|BE820934
EST:     CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAG                         GAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT
genomic: CTGATGTTGCTGCTACATTCAGCGGCATAATTCGTGCTCTGAAGGAGAAGgtgagcctat ... tacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatattaatttgcttagagtagagttaattgattgttgacctattacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGTCCCAACTACCAGAAGGGTCTAGCAAAAATGAGGGCACTCGGAGAGGAAA
                         ttaattgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcctatcatcatgaagctttgctctataatatcatattaatttgcttagagtagagttaattgattgttgacctattacaaaccagGAACAAAAGCTAAAAGAAGCAAAGATGCACATCTATGTGAGGAGAGGAGGTCCCAACTACCAGAAGGGTCTAGCAAAAATGAGGGCACTCGGAGAGGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA