Sequence
atgc intronic sequence ATGC exonic sequence...gcttttgatttatatttaatttattctctttgtaattagaccttatttagtcaatccttacattttgctttatcttttaattaatcgttttctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATTAAGATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCAGGTTAAAG
Basic information
species | Glycine max |
transcript | GLYMA16G09020.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g45590.1 (Oryza sativa), 3'ss of exon 5
gcttttgatttatatttaatttattctctttg--taattagaccttatttagtcaatccttac-attttgctttatcttttaattaatcgttttctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATTAAGATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCAGGTTAAAG
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---ctaaactgtttttgaacataactgtattgagtgctacaacttcatatgtttcatttagactatttcaagttctttgatcgtgatattcttcttgttctagGCTTATATGTTCAAGTATGATTCGACACATGGTCCATTTAAAGGCACCATAAAGGTTGTGGATGAGTCAACCTTGGAGATTAATGGGAAGAAAATTTCAG
upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 5
gcttttgatttatatt-taatttattctctttgtaattagaccttatttagtcaatccttacattttgctttatcttt---taattaatcgttttctcttgt--agGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATTAAGATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCAGGTTAAAG
| ||| | | | | || || | | ||| || || ||| || ||||| || ||||| ||||| || | |||| ||||||||||| ||||| || |||||||||||||| || || |||||||| || ||||||| || || |||| || ||||| ||| | || | |
-----taattcctgtcactgtgggagtaccaacccatccttccatgcggatgcaacatttg-gttgtgccttttctttctgtagataatctctttcttttttccagGCCTACATGTTCAAGTATGACTCCACTCATGGTCCATTTAAAGGCTCCATTAAGGTTGTGGATGATTCAACCCTGGAGATCAATGGAAAGAAAGTCACAA
upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 5
gcttttgatttatatttaatttattctctttgtaattagaccttatttagtcaatccttacattttgctttatcttt-taattaatcgttttctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATTAAGATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCAGGTTAAAG
|||| | | | | |||| | || | | | || || ||| | | | | || | ||| || |||| ||||||||||| ||||||||||||||||| | ||| || || || || | | ||||| || |||||||| || ||||| || || || ||||
-taactgatccacgtgcttgaacacgtaatattaatcatacttaaaggcatgggataatatatcaaacttaaaccaaatcttctctcctcctcttatgcagGCTTACATGTTCAAGTATGATTCTACTCATGGAAATTACAAAGGAACTATCAATGTAATTGATGATTCAACTTTGGAGATCAATGGAAAACAAGTCAAAG
upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 5
gcttttgatttatatttaatttattctctttgtaattagaccttatttagtcaatccttacattttgct--ttatcttttaattaatcgttttctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATTAAGATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCAGGTTAAAG
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--ttgtatggtagtttaggattcttgagctagttgttaggatccttcaactttagagagaaggaatggtagtgatatgttggttttcgtttattttacgcagGCTTACATGTTCAAGTATGATTCTACTCATGGAGTTTTCAAGGGAACCATCAAGGTATTGGATGAGTCCACTTTGGAAATCAATGGCAAGCAGATAAAAGMapped 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|254326010|gb|GR838891.1|GR838891EST: ATGTTGATGTTGTTGCAATTAATGATCCATTTATTGATGCAAAATATATG GCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATT
genomic: ATGTTGATGTTGTTGCAATTAATGATCCATTTATTGATGCAAAATATATGgtatgtaaat ... tctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATT
EST:
gi|254346561|gb|GR856283.1|GR856283EST: ATGTTGATGTTGTTGCAATTAATGATCCATTTATTGATGCAAAATATATG GCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATT
genomic: ATGTTGATGTTGTTGCAATTAATGATCCATTTATTGATGCAAAATATATGgtatgtaaat ... tctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttagtcaatccttacattttgctttatcttttaattaatcgttttctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATTAAGATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCAGGTTAAAG
tcgttttctcttgt CT-rich tract
ttacattttgctttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttttgatttatatttaatttattctctttgtaattagaccttatttagtcaatccttacattttgctttatcttttaattaatcgttttctcttgtagGCATACATGTTCAAATATGATTCTACTCATGGTCCATTCAAGGGGACCATTAAGATTTTGGATGACTCTACTTTGGAAATTAATGGGAAGCAGGTTAAAG
gcttttg
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