Sequence
atgc intronic sequence ATGC exonic sequencegtaagttattggactttatgacccattaattaacaagaaagatttttttgtaaactattctgcagtttttagtttacatacttaatttgctattctaattttgtggttaagGATATAGCAACAAGAGTTATTGCTCGTGAAGTTAATCTCGAAGAAACACCTGTTTCCAAGGTTATGACAAGGAATCCAGTATTTGTCCTTTCTGATACTC
Basic information
species | Glycine max |
transcript | GLYMA05G38140.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G38140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g69900.1 (Oryza sativa), 3'ss of exon 2
gtaagttatt-ggactttatgacccattaattaacaagaaagatttttttgtaaactattctgcagtttttagtttacatacttaatttgctattctaattttgtggttaagGATATAGCAACAAGAGTTATTGCTCGTGAAGTTAATCTCGAAGAAACACCTGTTTCCAAGGTTATGACAAGGAATCCAGTATTTGTCCTTTCTGATACTC
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----gtgatgaggattttctttgatgtatgtcctcaataggtgttgaattggaaa--attattcatttctcactct----------tttgctaacct-------ccaatcagGACATAACCACAAGAGTAATTGCTCGCGAATTGAAGCTAGAAGAGACACCTGTTTCAAAGGTCATGACAAGAAATCCTCTCTTTGTTCTGTCTGACACAC
upper sequence: GLYMA05G38140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 3
--gtaagttattggactt-tatgacccattaattaacaagaaagatttttttg-taaactattctgcagtttttag--tttacatacttaatttgctattctaattttgtggtt-aagGATATAGCAACAAGAGTTATTGCTCGTGAAGTTAATCTCGAAGAAACACCTGTTTCCAAGGTTATGACAAGGAATCCAGTATTTGTCCTTTCTGATACTC
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gtttgacttgaattactagtgagatatactgccaagccaaaaaaacttgcatgctacatttacctggatttttatggctttacttgtttcacaaaaccattcccttttgtggctgaagGACATAGCAACAAGAGTCATTGCTCGTGAACTTAATCTTGAGGAAACACCAGTCTCCAAAGTTATGACAAGGAACCCAATTTTTGTTCTTTCTGATACTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctgcagtttttagtttacatacttaatttgctattctaattttgtggttaagGATATAGCAACAAGAGTTATTGCTCGTGAAGTTAATCTCGAAGAAACACCTGTTTCCAAGGTTATGACAAGGAATCCAGTATTTGTCCTTTCTGATACTC
ttctaat putative branch site (score: 2)
tttttagtttacatac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttattggactttatgacccattaattaacaagaaagatttttttgtaaactattctgcagtttttagtttacatacttaatttgctattctaattttgtggttaagGATATAGCAACAAGAGTTATTGCTCGTGAAGTTAATCTCGAAGAAACACCTGTTTCCAAGGTTATGACAAGGAATCCAGTATTTGTCCTTTCTGATACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA