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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctattggatttgatcatttgagaaatgaaaatatatatttacattaagcatgtaaggttcattcttcatcttaccatctgtgtccttggttttatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG

Basic information

species Glycine max
transcript GLYMA09G35780.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G35780.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g07140.t01 (Vitis vinifera), 3'ss of exon 2
gtctattggatttgatcatttgagaaatgaaaatatatatttacattaagcatgtaaggttcattcttcatctt-accatctgtgtccttggttttatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG
||   ||  |    ||     |  ||||  | || | |||     | |  |||||  |  | ||||   ||    || |  |||||| |  ||||  | | |  ||| || ||||||||||| | ||||||||| |||||||| || ||||  ||||| |||||||||||||||||||
gtactttaaaaagtatatcaagtcaaattgatatttctataactttcatccatgtttgaattattcactatggggactaattgtgtcgt--gtttggtgtaa--gGCGCGTGCAAAACATGATACAACAAATACAGTTGTTGCGGGGTGTGTTACTGGGGGTGCAATATCAGCAAAAG
















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|208097326|gb|GD896295.1|GD896295
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGA
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGA
EST: gi|208243228|gb|GE040294.1|GE040294
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGA
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGA
EST: gi|298189377|gb|HO037780.1|HO037780
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|24136089|gb|BU926599.1|BU926599
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|208080316|gb|GD878912.1|GD878912
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACNTGACATAACAAATACCGTTGTTGCTGGA
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGA
EST: gi|298176547|gb|HO023134.1|HO023134
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGA
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGA
EST: gi|207748863|gb|GD719496.1|GD719496
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|26047885|gb|CA784534.1|CA784534
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|298188673|gb|HO035366.1|HO035366
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAAT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAAT
EST: gi|207795110|gb|GD763531.1|GD763531
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|208095152|gb|GD891966.1|GD891966
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAAC
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAAC
EST: gi|13790875|gb|BG653466.1|BG653466
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAA
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAA
EST: gi|193704363|gb|FK644785.1|FK644785
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACNTGACATAACAAATACCGTTGTTGCTGGA
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGA
EST: gi|31307580|gb|CD392783.1|CD392783
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
EST: gi|298169968|gb|HO018592.1|HO018592
EST:     TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAG                         GCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT
genomic: TTGCTGTTATGGGTTTCATATTCTCAGCTGCCGAGTGTGTTGTTGAGAAGgtctattgga ... tatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtaaggttcattcttcatcttaccatctgtgtccttggttttatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG
                    atcttac  putative branch site (score: 3)
                                          ttttatttc  putative PPT
                                          ttttatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctattggatttgatcatttgagaaatgaaaatatatatttacattaagcatgtaaggttcattcttcatcttaccatctgtgtccttggttttatttcacagGCTCGAGCAAAACATGACATAACAAATACCGTTGTTGCTGGATGTGCAACTGGAGGTGCAATATCAGCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG