Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
Basic information
species | Glycine max |
transcript | GLYMA05G34560.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 6
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgc--atgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
||| | || | || | || ||| | ||||| || || | || | ||| || | || ||| | ||||| |||||||||| ||||||||| ||| | || || || || || |||||||||||||| ||||| || ||||||||||| |||||||||||||||||||
-----------------gtaacatc-ctttactgttgctttcggataatctt--cactgttctgtacgcaaaaaagttgacccatgctaatctctaaccatggcac-acttagGAGGAAAGAAAAATTCTTGACCGTGAGCTTGCGCGGGCAAAAGTTACAGCAAACAGAGTTGCTGTTGTAGTTGCAAATGAGTGGAAAGATGCTAATGACA
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g44340.1 (Oryza sativa), 3'ss of exon 6
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacact-atat-agGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
|||||| | || | | || | || | ||||| || |||||| || || |||||| ||| |||| | | || || | |||||||||| ||||||||||| || || |||||||||| ||||| | ||||| ||||| || |||||||| ||||||||||||||||||| ||||| |
gtaatgcat--gatgccctgagcacacgttcctgat--gtttattc----------------tacctaatagaatggtaattgatgc-caatttacacttatgctgatgtcagGAAGAAAGGAAAACTCTTGATCGTGAACTAGCTCGTGCGAAGGTTTCGGCAAATAGAGTTGCAGTAGTGGTGGCAAATGAATGGAAAGATGGCAATGATA
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 6
gtaatgtgttaaa-tttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaa-agcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
|||| || ||| | | | | || | || | | | || | | || | || || | || || | | | | | || || |||| ||| ||| || ||||| | || | |||||||| || || ||||||||||| || ||||| |||||||| || || ||||||||| |||||||||
gtaacaacctattctttgactattgcatatgtcatcatgtcttcatgagctcttccccccttctataggaacagttcactcatgcttatttaacatttatgatcattac-cagGACCAAAAAAAGACACTTGAATGTGAACTTGCTCGTGCAAAAGTTACAGCAAACAGGGTTGCTGTTGTGGTTGCCAACGAGTGGAAAGATTCTAATGACA
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 2
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
||||| | || | | || | | | || | | ||| ||| |||| | | | || | || || ||| | | || ||||| |||| ||||||||||| || ||| |||||||||| ||||| ||||||| || || || |||||||| |||||||| |||||||||| |||| |
gtaatacatgaatcctgatgtccttggaaatgcattatgcgttttaggatatc-tacttgagcacc-atgactaatgcaagttttacaacgtttcct---attct---tagGAGGAAATGAAAACTCTTGATCGTGAGCTAGCTCGTGCAAAGGTTTCAGCAAATAGGGTTGCAGTAGTGGTGGCAAATGAGTGGAAAGATGGCGATGATA
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G68060.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcat--cttaattgttgcatgatttgttttgacacta----tatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
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----------------------------------gtaagttaataca-tttccgaaaaaagaagtatagaatctttactcaactgatgaaggaatatttcttgctctacttttgcagGAAGAACGAAAAACTCTTGACCGGGAACTTGCGCGTGCAAAGGTTACAGCAAACAGAGTTGCGACAGTGGTTGCAAATGAATGGAAAGATGGTAATGATA
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
| || || ||| | || | | || | || | ||| || |||| | ||| || ||||||| | ||||||| | |||||||||||||| ||| | || ||||| ||||| |||||||||||||| || ||||| |||||||| |||||||||| |||||| |
-------------gtaactaaacacact-tcataaagtctctaatttcttgtcacaacaatt-gcctactgatgtaggaataatt------cttgtttt--tgtctttcagGAAGAGCGGAAAACTCTTGACCGGGAGCTTGCACGTGCAAAGGTTACAGCAAACAGAGTTGCCACTGTGGTAGCAAATGAGTGGAAAGATGGTAATGATA
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 6
gtaatgtgttaaatttac-caac-----tttactcttctagtttgttt---actca-attattaca-ctgatccacctaa---aagcatctta--attgttgcatgatttgttttgacactata------tagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
|||||||| | |||| ||| || | || | | ||| || | ||| || || || | | || | | | || ||||||| | | | | | | | |||| ||||||||||| || ||| | ||| | || ||||| |||||||| |||||||| || || ||||| || ||||||||||||||||||||||||||||
gtaatgtgccatttttaaacaataaatattgaacattgcaagtcatttcaggcttatatttttgcatctagttggcatatgccatgtgttctatcattgttgagttgtctttccttttcttttggaccttcagGAGGAAAGAAAAACCCTCGACAGGGAGCTGGCCCGTGCAAAGGTAACTGCAAACAGGGTGGCAGTAGTTGTAGCAAATGAATGGAAAGATGCTAATGACA
upper sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ18059 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
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------------------------------------------------gtagtgccgccagccacctttggg--tcgcactcaccccaca--ttgtctttttaccat-tagGAAGAGAAACGGACGCTTGAGCGGGAACTGGCGCGTGCCAAGGTAACAGCAAACAGAGTGGCAGTCGTCGTTGCAAACGAATGGAAGGATGCAAACGACAMapped 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|193700394|gb|FK636353.1|FK636353EST: CAGCTGCCAATGCTGTGAGAGATTATCAACGGAAAGTTCAAGAAATGAAT GAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCA
genomic: CAGCTGCCAATGCTGTGAGAGATTATCAACGGAAAGTTCAAGAAATGAATgtaatgtgtt ... cactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
ttttgac putative branch site (score: 3)
atcttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtgttaaatttaccaactttactcttctagtttgtttactcaattattacactgatccacctaaaagcatcttaattgttgcatgatttgttttgacactatatagGAAGAAAGAAAAACTCTTGACCGAGAGTTAGCTCGTGCCAAGGTAACAGCAAACAGAGTAGCTGTAGTGGTTGCAAATGAATGGAAAGATGCTAATGACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG