Sequence
atgc intronic sequence ATGC exonic sequencetgtgttggatatgctttaaaatctcatacatatttatttttattacattcctttattgacaaggttttgaaatgcctcgagtgcagaTATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAG
Basic information
species | Glycine max |
transcript | GLYMA18G31780.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G079256_T02 (Zea mays), 3'ss of exon 9
tgtgttggatatgctttaaaatctcatacatatttatttttattacattcctttattgacaaggttttgaaatgcctcgagtgcagaTATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAG
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------gtaattatttctttgttgatttcacagctaagctatcagcgctcgttacttatgattgttttgg--tgattgctttgtagCTACGGTGGTGGTATGAGTTCAGCAAAAGCAGCTCTTGAGAGTGATACAAGA-
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 3'ss of exon 8
-----------tgtgttggatatgctttaaaatctcatacatatttatttttattacattcctt---tattgacaaggttttgaaatgcctcgagtgcagaTATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAG
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gtaaggatggcttcttcacaagttattcaaaggaacaaactaatgcacacacataacgatgtcaacacattctcacaagtatctctttcattctgtgcagGTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGG-
upper sequence: GLYMA18G31780.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 9
tgtgttggatatgctttaaaatctcatacatatttat-ttttattacattcctttattgacaaggttttgaaatgcctcgagtg-------cagaTATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAG
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---gtatagcctgttgctttatttcctccatcttcatgttttgacgagtaccacttctcgtaggatcacatagtgtttaaattgtcacctgcagATATGGGGGAGGCATGAGTTCAGCCAAAGCCGCTCTAGAAAGTGATACACGA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttttattacattcctttattgacaaggttttgaaatgcctcgagtgcagaTATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAG
tattgac putative branch site (score: 2)
ttttattacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgttggatatgctttaaaatctcatacatatttatttttattacattcctttattgacaaggttttgaaatgcctcgagtgcagaTATGGTGGTGGTATGAGTTCTGCAAAAGCTGCTTTAGAAAGTGATACAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT