Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttgtctttatatgcctattaatgttaaaaagtattatattttaaagatttttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
Basic information
species | Glycine max |
transcript | GLYMA06G39770.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G20630.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgttttgtctttatatgcctattaatgttaaaaagtattatattttaaagatttttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
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gtctctttctttctgaaacaatgatccttataatgttcccctattgtccctgtatataaatacttattatcctttcttga-----tttactgtggcagATGTATACATTGATGTTCCGGATGTTATTGATATCAGCCACATGCGTAGCAAAGGACTCCAACCTGGGGAAGAACTGTTGCCAGATGGCG
upper sequence: GLYMA06G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv19s0014g03910.t01 (Vitis vinifera), 3'ss of exon 2
gtatgttttgtctttatatgcctattaatgttaaaaagt--attatattttaaagatt---tttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
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---cctccttgcaaagcaaattttttaacattattacttttgttttacttgaaatgtgcaattattaattattaccacgtttttatcatatttgactgtccagATGTCTACATAGATGTTCCTGATATCATTGATATTAGTCACATGCGTAGCAGGGGCATTCAGCCTGGGGAAGAGCTATTACCAGAGGCTG
upper sequence: GLYMA06G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv03s0017g00960.t01 (Vitis vinifera), 3'ss of exon 2
gtatgttttgtctttatatgcctattaatgttaaaaagtattatattttaaagatttttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
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-------------------------------------gtatctttcatacaggactgtt--ggtcta---actt-------catatttgactgtccagATGTCTACATAGATGTTCCTGATATCATTGATATTAGTCACATGCGTAGCAAGGGCATTCAGCCTGGGGAAGGGCTATTACCAGAGGCTG
upper sequence: GLYMA06G39770.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv19s0014g03920.t01 (Vitis vinifera), 3'ss of exon 15
gtatgttt----tgtctttatatgcctattaatg----------ttaaaaagtatta---------tattttaaagatt---tttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
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gtatctttcatgtgcctttatttgcctccttgcaaagcaatttttttaacattattacttttgttttacttgaaatgtgcaattattaattattactacgtttttatcatatttgactgtccagATGTCTACATAGATGTTCCTGATATCATTGATATTAGTCACATGCGTAGCAGGGGCATTCAGCCTGGGGAAGAGCTATTACCAGAGGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattttaaagatttttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
ttctgat putative branch site (score: 3)
catttttcttctttc putative PPT
taaagatttttctgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttttgtctttatatgcctattaatgttaaaaagtattatattttaaagatttttctgatctatatattttgttaagcatttttcttctttcagATGTGCACATTGATGTTCCTGATATCATAGATATCAGTCACATGCGCAGCAAAGGTCAGCAGTCTGGGGAAGAGCTATTACCTGATGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT