Sequence
atgc intronic sequence ATGC exonic sequencegtgattgaccatttcagttactcacatttgcttttatacggtagagtatatgttccgtatgagggttgatgaatattttgggcacaacttttgaaactcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCAGAGGATGCATTATCACAAG
Basic information
species | Glycine max |
transcript | GLYMA20G24770.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G24770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g41640.1 (Oryza sativa), 3'ss of exon 1
gtgattgaccatttcagttactcac---atttgcttttatacggtagagtatatgttccgtatgagggttgatga-atattttgggcacaacttttgaaactcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCAGAGGATGCATTATCACAAG
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--gtttgacacgagtgatcacccacccaattcagtaacaagcaaagaatctgaagctaccattgactgctattgttgaatgatgatgatgatgttgtttgtgcagGTACTTGAGAGCCATCTTGAGCCGCTGACGAATCAGCAGTTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCACAGG
upper sequence: GLYMA20G24770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g15480.2 (Oryza sativa), 3'ss of exon 7
gtgattgaccatttcagttactcacatttgcttttatacggtagagtatatgttccgtatgagggttgatgaatattttgggcacaacttttgaaactcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCAGAGGATGCATTATCACAAG
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gtt-ttgacacgatcgagtgatcacccacccaattcagcaacaagcaaagaatctgaagctaccattgaccgccattgttgatgatgttgtttgtgc--agGTTCTTGCCAGCCATCTTGAGCCGCTGACGGATCAGCAGCTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCGCAGG
upper sequence: GLYMA20G24770.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G68640.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgattgaccatttcagttactcacatttgcttttatacggtagagtatatgttccgtatgagggttgatgaatattttgggcacaacttttgaaactcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCAGAGGATGCATTATCACAAG
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gtaaaagaaagggtt--caaaacattttcacaatcattggttttgatttttttttctcataa---ttggtaactatgttg-----------------ttagATATTGGGGAACCATGTGGATCCATTGACGGACCAGCAGTTGATAGGCATTTGCAACCTTCAGCAATCGTCTCAACAAGCAGAGGATGCATTGTCACAAG
upper sequence: GLYMA20G24770.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g03230.t01 (Vitis vinifera), 3'ss of exon 9
-------------------gtgattgacc----atttcagttactcacatttgcttttatacggtagagtatatgttccgtatgag-ggttgatgaatattttgggcacaacttttgaaactcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCAGAGGATGCATTATCACAAG
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gtaatttgaagatttattgcttttagaccttgaatcttttttatccagttctgcaatggc-tgaaggaatgtatagtttttttggttgattcacatctatttctattttatttttggagtttcagATACTTGGGAACCAACTTGAACCTTTAACAGATCAGCAGCTGATGGGCATATGTAATCTACAACAGTCCTCACAGCAAGCTGAGGATGCATTATCACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatgttccgtatgagggttgatgaatattttgggcacaacttttgaaactcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCAGAGGATGCATTATCACAAG
ggttgat putative branch site (score: 5)
ctttt putative PPT
ttgatgaatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattgaccatttcagttactcacatttgcttttatacggtagagtatatgttccgtatgagggttgatgaatattttgggcacaacttttgaaactcagATAGTTAGAAACCAGCTTGAGCCGTTAACCGAACAGCAGTTGATGGGCATTTACAATCTGCAGCAGTCTTCCCAGCAGGCAGAGGATGCATTATCACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG