Sequence
atgc intronic sequence ATGC exonic sequence...ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatgtttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
Basic information
species | Glycine max |
transcript | GLYMA14G01610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G01610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G26590.1 (Arabidopsis thaliana), 3'ss of exon 2
ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatgtttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
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-------gtatgtatacacaatatacaat-ataattcaaaaattacatagtttttgtttgtaacagttacat-tatttatctgt---------catgtagTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG
upper sequence: GLYMA14G01610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G55930.1 (Arabidopsis thaliana), 3'ss of exon 2
-ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatgttt----agATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
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tgtgggtaatagtcatttaaatactagaactatggcctaagaaacaaatattttta-----acgatttgtgatctttaagactttaacaatcatttcttttgcagTTGTTGGGATATGGATGGGCTGGAATCTTCAGGAAGTTCCTTGTGGATTCACCGTATATGTGGTGGCCGTCAAATTTGGTTCAAGTCTCACTCTTTAG
upper sequence: GLYMA14G01610.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g00860.t01 (Vitis vinifera), 3'ss of exon 2
--------ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatgtttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
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tgtagtatatggtttactcatactactaatccaccaattaatttgatattttagt-ttctcttgttcaccttgatagtttctcttc-----ttctattgaa--ttcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAG
upper sequence: GLYMA14G01610.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g00870.t01 (Vitis vinifera), 3'ss of exon 1
ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatg--tttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
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-atatattacttattttgtagtatatggtttccaccaat-taatttgatattttaatttctcttgttgaccttcatagtttctcttcttctattgaattcagTTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAGMapped 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|209704053|gb|BW673653.1|BW673653EST: ACAGGAATATCCATCCACTTGCCGCTTTTCTCTTAGCACTTTCCACCCAG ATGCTTGGTTATGGA
genomic: ACAGGAATATCCATCCACTTGCCGCTTTTCTCTTAGCACTTTCCACCCAGgtcaacattc ... gaatgtttagATGCTTGGTTATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatgtttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
tgctaaa putative branch site (score: 2)
tctattatagaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaatccacttttctttgtattttacaatcaaaatttctataatagaactctctattatagaaaaatgaaatctgctaaaccgtgtcgttgaatgtttagATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaacc