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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcctgactgagtatattcctctggtttattagttttaattgatttaaaagtcaattttatgtatcattgcaaagctggtaaatagcatgtcacg...

Basic information

species Glycine max
transcript GLYMA06G08640.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08640.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os05g13440.1 (Oryza sativa), 5'ss of exon 3
CATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcctgactgagt-atattcctctggtttattagttttaa---ttgatttaaaagtcaattttatgtatcattgcaaagctggtaaatagcatgtcacg-
|| || ||| | ||  |  | ||||| |||||  | |||||| | ||||| | | | || ||||||||||| |||||||| ||||| ||||| |||||||||         | |   | ||| | || |  |    | |||  ||   ||  |||     ||  |  | ||  || |||  |  |   |  |     | | ||  
CACGTGTATTTGAGATTAAATAAAGGTCAGACAATGGATGACATAAGTGAAGGTGTGCTTGAAGATTGTGCCCAGCTTGTGAAAGCTAATTCCATTCAAGgttgggaa--aattacatgataattctgtaatac-ctggttcaaaccttttgttttgctttccctagtttggttctttgtcagacacatttaattatttttacag

upper sequence: GLYMA06G08640.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G157332_T05 (Zea mays), 5'ss of exon 2
CATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgt-----aaatgcctgactgagtatattcc-tctggtttattagttttaattgatttaaaagtcaattttatgtatcattgcaaagctggtaaatagcatgtcacg----------------
||||| ||||| ||  || | ||||| ||  |  | |||||| ||||||||| ||| |||||||| ||||| |||||||||||||| ||||| |||||||||     |||   |  |  ||  |||||   ||     | || | || | ||  | |   |   ||| |    ||  |     |  | || | ||   |||                     
CATGTGTATGTGAGATTGAATAAAGGTCAATCAATGGATGACATGAGTGAGGGTTTGCTGGAAGACTGTGCGCAGCTTGTCAAAGCTAATTCCATTCAAGgttggacaaactacaaagagacaatattatatcacaaattttggcttcattttttcttgcaag-aatgtggaatacaagctgtagtccggcacatgtgatgatttcttcatttttggtgcag

upper sequence: GLYMA06G08640.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv04s0008g03810.t01 (Vitis vinifera), 5'ss of exon 2
CATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcctgactgagtatattcctctggtttattagttttaattgatttaaaagtcaattttatgtatcattgcaaagctggtaaatagcatgtcacg
||||| ||||| ||  ||||||| || |||||  | |||||  | ||||| | ||||||||| |||||||||||||||||||||||||| || || ||||| |||       | || | | ||  | |   || ||| |     ||| ||| |        | ||| ||   |       || | || ||   |  | | 
CATGTTTATGTAAGATTGCACAAGGGTCAGACAATTGATGATATAAGTGAAGGTTTACTGGAGGATTGTGCTCAGCTTGTCAAAGCAAACTCCATCCAAGgcaaaatatgctcagactctttttttatttatttttattacattttgttttcacgtatttgtctatttaatctatgtggtctagcaagtattctacctca

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|120534483|gb|EH262616.1|EH262616
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|298183696|gb|HO028909.1|HO028909
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAGTGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|298164673|gb|HO014318.1|HO014318
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|298173543|gb|HO016879.1|HO016879
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCCATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|151411303|gb|EV281114.1|EV281114
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|151412239|gb|EV282051.1|EV282051
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|6455553|gb|AW186236.1|AW186236
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|58016161|gb|CX702903.1|CX702903
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|151394766|gb|EV264637.1|EV264637
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|58015274|gb|CX702016.1|CX702016
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|18734019|gb|BM527940.1|BM527940
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|120534643|gb|EH262776.1|EH262776
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
EST: gi|298168083|gb|HO013346.1|HO013346
EST:     GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAG                         GAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA
genomic: GGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcct ... ttcatggcagGAAATAAAGTGAACAATGTTGATGTTGTTTACACTCCCTGGTCTAATTTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGTCTATGTCAGGCTGCACAAAGGCCAGACTCTCGATGACCTGAGTGAGGCTTTACTGGAAGATTGTGCTCAGCTTGTCAAAGCAAATTCAATTCAAGgtaaatgcctgactgagtatattcctctggtttattagttttaattgatttaaaagtcaattttatgtatcattgcaaagctggtaaatagcatgtcacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA