Sequence
atgc intronic sequence ATGC exonic sequencegttgaattgaggcctggaaattgttgattgaagttattaacatttactttctcctagtggttgacttttataatattcttgtcttttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
Basic information
species | Glycine max |
transcript | GLYMA18G51810.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
--gttgaattgagg----cctggaaattgttgattgaagttat--taacatttactttc---tcctagtg-gttgacttttataatattcttgtcttttca-tcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagcatggaaattcatgtcatattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 11
gttgaattgaggcctggaaattgttgattgaagttattaacatttactttctcctagtggttgacttttataatattcttgtcttttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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-------------gtaccacttcctggttca--ctaggaattaaagcttcatgcagacattctagtactgtcattcctgaaacaaagtatatgttcagGTCCAGACCATTCGTCAAGGTTACCTCTCGAAAAGATCTTCAAACTTGAGAGCTGATTGGAAAAGAAGGTTTTTTGTCCTTGATAGTCGAGGAATGCTGT
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
gttgaattgaggcctggaaattgttgattgaagttattaacatttactttctcctagtggttgacttttataatattcttgtcttttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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----------------------gttgatcaacgtctttaacatatgattgatacatcttccaga---gagtactattaacatttcttggtgctttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT
upper sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------------gttgaattgaggcctggaaattgttgattgaagttattaacatttactttctcctagtggttgacttttataatattcttgtct---tttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
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gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTATMapped 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|21637852|gb|BM108007.1|BM108007EST: GTTCACATAAGATGATAGAGGCAGTTATGCAATCTGCTGCCAAGGGAAAG GTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGG
genomic: GTTCACATAAGATGATAGAGGCAGTTATGCAATCTGCTGCCAAGGGAAAGgttgaattga ... atcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactttctcctagtggttgacttttataatattcttgtcttttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
ggttgac putative branch site (score: 4)
ttcttgtcttttcatc putative PPT
ttttataatattcttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaattgaggcctggaaattgttgattgaagttattaacatttactttctcctagtggttgacttttataatattcttgtcttttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG