Sequence
atgc intronic sequence ATGC exonic sequence...ttcattattgtatcacaattatataaatctcatgctaatgccctataatactctgtgcaaaggctgttgtgaagcaaatctccttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
Basic information
species | Glycine max |
transcript | GLYMA05G28660.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
ttcattattgtatcacaattatataaatctcatgctaat-gccctataatactctg-tgcaaaggctgttgtgaagcaaatctc-cttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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---gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
ttcattattgtatcacaattatataaatct-catgctaatgccctataatactctg-tgcaaaggctgttgtgaagcaaatctc-cttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG-
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---gttctagtacgcgcaccctatgtttgtatttttcaccagcttgcatcattctgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G13730.2 (Arabidopsis thaliana), 3'ss of exon 4
----------ttcattattgtatcacaattatataaatctcatgctaatgccctataatactctgtgcaaaggctgttgtgaagcaaatctccttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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aaaagatccttttctcttcctgttttagtaaagtaattcc---gtttttgttgcatataaagctgcaaaatgaccttcctga-------tttcaacttgatactgttcagGACACAGAAGTTTTGGAACAAATAGAACGCGATGTGATGCGTACTCATCCAGATATGCACTTTTTCTCTGGGGATTCAGCAGTTGCAAAATCTAATCAG
upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
ttcattattgtatcacaatta--tataaatctcatgctaatgccctataatactctgt-gcaaaggctgttgtgaagcaaatctccttctttgcat-tttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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cccatttctttatgctattggactataaat----tggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ15182 (Selaginella moellendorffii), 3'ss of exon 4
ttcattattgtatcacaattatataaatctcatgctaatgccctataatactctgtgcaaaggctgttgtgaagcaaatctccttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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---------------------------------------gtttgtttacttcctttgcaattccaatccaaatggaa---------tttccacttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAG
upper sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ09811 (Selaginella moellendorffii), 3'ss of exon 4
ttcattattgtatcacaattatataaatctcatgctaatgccctataatactctgtgcaaaggctgttgtgaagcaaatctccttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
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---------------------------------------gtttgtttacttcctttgcat------ttccaatccaaatagaa---tttccacttcgcagGACACGGAACTTTTCGAGCAGATTGATCGTGATGTTAAGCGAACTCATCCTGATATGCAGTTTTTCTGTGGTGATAACGAGCGCGCGCACGAAAACCAGMapped 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|13481526|gb|BG510869.1|BG510869EST: AGCATCCTTTGAGTCTTGGGAAGACCAGCGTATGGAATCAGTTCTTCCAG GATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCT
genomic: AGCATCCTTTGAGTCTTGGGAAGACCAGCGTATGGAATCAGTTCTTCCAGgtagactgta ... cattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatactctgtgcaaaggctgttgtgaagcaaatctccttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
tctccttctttgcatt CT-rich tract
attttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcattattgtatcacaattatataaatctcatgctaatgccctataatactctgtgcaaaggctgttgtgaagcaaatctccttctttgcattttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
- - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - aatgccc
- - - - - - - - - - - - - - - - - - - - - - - - - -tctgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagcaaa