Sequence
atgc intronic sequence ATGC exonic sequencegtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
Basic information
species | Glycine max |
transcript | GLYMA12G03490.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
--gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcat-taatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
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gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgc--atgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT--
|| | || | | || || ||| | | | | | | | | || | | | || || | || | || | ||||| || | || || || ||||| || || |||||||| |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||| ||
---------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgt-gtgtgcttctgctgctctacttgttgc-------agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
|| | || | | || || ||| | | | | | | | | || | | | || || | || | || | ||||| || | || || || ||||| || || |||||||| |||| || || || || ||||||||||||||||||||||| ||||| || || |||||||| ||
---------------gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgt-gtgtgcttctgctgctctacttgttgc-------agGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgt-tattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
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-------------------------------ttaatgcataaatgttatatacttgta----gagttgtagataat-tgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattatt--aatgatatgaaactgtcattaata--tagtagtaatgctatgtttttccaattgttatt--atgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
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------------------------------------gtactatacatat-atctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
cattaat putative branch site (score: 3)
attaatatagtagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgttattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT