Sequence
atgc intronic sequence ATGC exonic sequence...aagaagagaaacaagaggatgtgaattataaaaagaaaattatgaaaaagtgttgtaaagagagtgaatgaaataacattattctgttgatttaatctagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
Basic information
species | Glycine max |
transcript | GLYMA06G45640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G45640.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G061515_T01 (Zea mays), 3'ss of exon 1
---------------------aagaagagaaacaagaggatgtg---aattataaaaagaaaattatgaaaaagtgttgtaaagagagtgaatgaaataacattattctgttgatttaatctagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
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gtagtatattcatccctcacgtacgatcacaacgctgtgatgcatgcggctgtggaatcaaaattt--aacggacatgggaacatgtactgatttataactgaggatgtttgtgtgtgaaccagCTCTGGAACATCCGGAGGGGAGAGGAAGCTGATGCCGACCATCGCCGACGAGCTGGACAGGAGGTCGTTGCTGTATAGCCTGCAGATGCCGGTGATGAGC
upper sequence: GLYMA06G45640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
aagaagagaaacaagaggatgtgaattataaaaag-aaaattatgaaaaagtgttgtaaagagagtgaatgaaataacattat-tctgttgatttaatct---agCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
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-----gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
upper sequence: GLYMA06G45640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G54510.1 (Arabidopsis thaliana), 3'ss of exon 1
aagaagagaaacaagaggatgtgaattataaaaagaaaattatgaaaaagtgttgtaaagagagtgaatgaaataacattatt-ctgttgattta-atc--tagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
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--tccattcactgttaaaacctttatc-caaaaagaaaatttttaatgggt-ctacttttatctttcatatattcacaaaagaattattgatatatgtcaacagTTCTGGGACTTCTGGTGGAGAGAGGAAACTGATGCCAACAATCGAAGAGGAACTAGACAGAAGATCACTTCTCTACAGTCTCTTGATGCCTGTGATGGAC
upper sequence: GLYMA06G45640.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0134g00230.t01 (Vitis vinifera), 3'ss of exon 1
aagaagagaaacaagaggatgtgaattataaaaagaaaattatgaaaaagtgttgtaaagagagtgaatgaaataaca-ttattctgttgatttaatctagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
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---gtgagtgtgtgtggcttacttctttcagaattgaaatt--tgatccgttttgagttctgtgttttggaattgtgagttgttttgatgtgtgggtgcagTTCTGGAACTTCTGGCGGAGAGAGAAAACTGATGCCCACCATTGAAGAGGAGCTCGGGAGGAGGTCTTTGCTGTATAGCCTGCTGATGCCTGTGATGAACMapped 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|209702758|gb|BW652774.1|BW652774EST: GATGCCTCCCCAATTTTATGTTCCAAACCTATTTCTGAGTTCCTCACTAG CTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGA
genomic: GATGCCTCCCCAATTTTATGTTCCAAACCTATTTCTGAGTTCCTCACTAGgtcagtatat ... tttaatctagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagtgttgtaaagagagtgaatgaaataacattattctgttgatttaatctagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
aatgaaataacattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagaagagaaacaagaggatgtgaattataaaaagaaaattatgaaaaagtgttgtaaagagagtgaatgaaataacattattctgttgatttaatctagCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - -gagaaac
- - - - - - - gaggatg
- - - - - - - - - - - - - -ataaaaa
- - - - - - - - - - - - - - - - - - - - - -gaaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatga