Sequence
atgc intronic sequence ATGC exonic sequence...aaaaagttgttccaaataagaccttaattaaaatgttttatttcaaaattatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
Basic information
species | Glycine max |
transcript | GLYMA09G34470.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
aaaaagttgttccaaataagaccttaattaaaatgttttatttcaaaat----tatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
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----aataaatctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
upper sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 1
----------aaaaagttgttccaaataagaccttaattaaaatgttttatttcaaaattatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
| || || | || | | |||| ||| || || | | | ||| ||| ||| | ||||| || ||||| || || |||| ||| |||||||||| ||||| ||||| || ||| |||||| ||||||||||||| ||||||||||||||||||||||| ||| || ||||| |
aaaataaaaaataagaacatttcttattttgcttccattataat--ttgatattgacaatat-ttaaaatggatatcgattaattttt-tacaaattatttc------agCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCACTTGAACCAGGAAGAGTGACATTTGATGAGAAGATGGTTGTGAGGAAGG
upper sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0033g00270.t01 (Vitis vinifera), 3'ss of exon 1
aaaaagttgttccaaataagaccttaattaaaatgttttatttcaaaattatattagaatcacatttttttaatcattatacaatttggttt-----ttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
||| || | | || || || |||| ||||| ||| | |||| | | | | | || || || | || ||||| |||||||||||||| ||||| |||||||| | |||||| ||||||||||||| ||||||||| ||||||||||||| |||| || ||||| |
tcttagtaatttccc-cactcttttgatgggcctgcattat----aaattctatcaatatcaaactctaagattgatactaattttgagcaaaaaaatttggtagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCATCCAGAATGGGAGATGCACTTGAACCAGGAAGAGTGTCATTTGATGAGAAGATGATTGTGAGGAAGG
upper sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 1
----aaaaagttgttccaaataagaccttaattaaaatgt-tttatttcaaaattatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
| | || || | ||| |||||| | | | || | |||| | || |||| ||| | | ||| |||| |||||||||||||| ||||| |||||||| ||| |||||| ||||||||||||| |||||||| |||||||||||||| |||| || |||| |
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatca--acatcaaaatctaagattgataataattgtgta---caaaattttggcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG
upper sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0053g00460.t01 (Vitis vinifera), 3'ss of exon 1
-aaaaagttgttccaaataagaccttaattaaaatgttt-tatttcaaaattatattagaatcacatttttttaatcattatacaatttggtt----tttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
||| || | | || || || | ||||| ||| ||| | |||| | | | || || | |||| || ||| |||| |||||||||||||| ||||| |||||||| ||| |||||| ||||||||||||| |||||||| |||||||||||||| |||| || ||||| |
ctcctagtaatttcct-cacccttttgatgggcctgcctgtattt----attctatcaacatcaaaaatctaagattgata-ataattgtgtcaaaattttggcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAAGGMapped 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|298170317|gb|HO018941.1|HO018941EST: TGGTGCAGCTCAAACTTGTGGAGGCCATCAAGGCTGCAGGGAACGTTAAG CGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCA
genomic: TGGTGCAGCTCAAACTTGTGGAGGCCATCAAGGCTGCAGGGAACGTTAAGgtatgttgta ... ttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaattatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
ttttaat putative branch site (score: 3)
tttggtttttctct putative PPT
atattagaatcacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaagttgttccaaataagaccttaattaaaatgttttatttcaaaattatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - -ccaaata