Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttggatatgctttaaaatctcatatacatgtttatttttattacattcttttattgacaaggttttgaaatgccttatatgcagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGA
Basic information
species | Glycine max |
transcript | GLYMA08G45990.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G079256_T02 (Zea mays), 3'ss of exon 9
gtgtgttggatatgctttaaaatctcatatacatgtttatttttattacattcttttattgacaaggttttgaaatgccttatatgcagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGA
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-----gtaattatttctt----tgttgatttcacagctaagctatcagcgctcgttacttatgattgttttgg--tgattgctttgtagCTACGGTGGTGGTATGAGTTCAGCAAAAGCAGCTCTTGAGAGTGATACAAGA
upper sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 8
----------gtgtgttggatatgctttaaaatctcatatacatgtttatttttatt-acattcttttattgacaaggttttgaaatgccttatatgcagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGA
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gtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcagGTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGG
upper sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 9
gtgtgttggatat-gctttaaaatctc-atatacatgttt--atttttattacat-tcttttattgacaaggttttgaaatgccttatatgcagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGA
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--gtatagcctgttgctttatttcctccatcttcatgttttgacgagtaccacttctcgtaggatcacatagtgtttaaat-tgtcacctgcagATATGGGGGAGGCATGAGTTCAGCCAAAGCCGCTCTAGAAAGTGATACACGAMapped 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|16345261|gb|BI970856.1|BI970856EST: GGATCTGCAATTTCTCTTACATACATTGCTTCAGAAAGGATCATTCCTGG ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAG
genomic: GGATCTGCAATTTCTCTTACATACATTGCTTCAGAAAGGATCATTCCTGGgtgtgttgga ... ttatatgcagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttatttttattacattcttttattgacaaggttttgaaatgccttatatgcagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGA
tattgac putative branch site (score: 2)
tttttattacattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttggatatgctttaaaatctcatatacatgtttatttttattacattcttttattgacaaggttttgaaatgccttatatgcagATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT