Sequence
atgc intronic sequence ATGC exonic sequencegtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
Basic information
species | Glycine max |
transcript | GLYMA08G22140.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaata-tgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
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----------------------------------------------------------------------------gtaattt---cttaatcttctgctcttatct--ttgcattgaaaagtgt--gcttccatccagaaaacattttctgt------tattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
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---------------------------------------------------------------------------------------------tcttattttcagac--ttacgcgacactgttt--aatttgtagga-gctatgtgttttatt--atctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
||| || || ||| | || || | | || | ||| || ||| | |||||||||| ||||||| || ||||| |||||||||||||||||||| | ||| | ||||| |||||||||||||| ||| |||| ||| |||||||| ||
-------------------------------------------------------------------------------------------------------------------gttcctttcaaatctttttaggttttagtgtaatgtggtcaaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgca-tgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
| | | | || || | || | | | || || |||| | || ||| ||| || | | ||||||||||||||||| || ||||| || ||||||||||| ||||| | ||| | ||||| |||||||||||||| ||| |||||||| | || || |||
--------------------------------------------------------------------------------------------------------------------gttat-tttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 21
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
| | | | | | | || | ||| | | | | | |||| | | | ||| | | | ||| | | ||| ||||||||||||||||| || ||||| |||||||||||||| |||||||||||||| ||||| || |||||||||| ||||| |||||||||||| | | |
-----------------------------------------------------------------------------------------------atatgcctgcttgggtagttggatctatttca----tttaacttttcttgtgatttaaa-gaaagagacacatatctaatcctgtttgatcaacactatatgcagGTTAATCCAAAAGCTGCTGAATCTTTGGCTGATCCTGAAGAGTATCCTAATTTATTTGAGGACTGGCAAGTTGGTCTTGCCATTGAATCTAAAGTTGCCG
upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctg-gattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatt-tgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
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------------------------------------------------------------------------------------------------------catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAGMapped 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|151397194|gb|EV267067.1|EV267067EST: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG GTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAAT
genomic: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatgttat ... atatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAAT
EST:
gi|151411223|gb|EV281034.1|EV281034EST: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG GTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAAT
genomic: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatgttat ... atatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAAT
EST:
gi|192294532|gb|FG987461.1|FG987461EST: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG GTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAAT
genomic: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatgttat ... atatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
tgttaat putative branch site (score: 3)
aaataaaaatataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT