Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatgaattttggttttgggttcatatatactactgcatagtaatttcttatttgtgtgctacttatctgatgcaattgttgtttgtgtttattgcttgaaagtttattggagaagactgaagaatatctgttgtacatcttgatataaaagttgacatgatttattcatttggttcctagAAAGTATTTTGGCGAGGGGTAGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAGTGCCAAG
Basic information
species | Glycine max |
transcript | GLYMA12G04480.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 4
gtatgtatgaattttggttttgggttcatatatactactgcatagtaatttcttatttgtgtgctacttatctgatgcaattgttgtttgtgtttattgcttgaaagtttattggagaagactgaagaatatctgttgtacatcttgatataaaagttgacatgatttattcatttggttcctagAAAGTATTTTGGCGAGGGGTAGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAGTGCCAAG
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----------------------------------------------------------------------------ccaatccaaagtccaaaataaagtttgaagaactattatatgttaccata---tatttagctaccaattctttattaatgg-aacaacatgtgctctttaa-----cagAGGGTATTTTGGCGTGGTGTTGTCGAAGAACTCCTTTGGTTCATCAGTGGCTCAACAAATGCAAAG
upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtatgaattttggttttgggttcatatatactactgcatagtaatttcttatttgtgtgctacttatc--tgatgcaattgttgtttgtgtttattgc-ttgaaagtttattggagaagactgaagaatatctgttgtacatcttgatataaaagttgacatgatttattcatttggttcc-tagAAAGTATTTTGGCGAGGGGTAGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAGTGCCAAG
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gtatatatttttcaaaatgaagatttcctttacaaataattgtattagtttgttctgtgggtatttccttccgtttctcagaagtttggttttatttgatgcattatgagtgaaattcaagtgaaaaaggaatattttttgtcaa--ttcatatgttagtttacacatttttattgtttgctttgatagAAAGTATTTTGGCGAGGGGTTGTTGAAGAACTGCTGTGGTTCATCAGTGGCTCAACAAATGCTAAG
upper sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtatgaattttggttttgggttcatatatactactgcatagtaatttcttatttgtgtgctacttatctgatgcaattgttgtttgtgtttattgcttgaaagtttattggagaagactgaagaatatctgttgtacatct-tgatataaaagttgacatgatttattcatttgg---ttcctagAAAGTATTTTGGCGAGGGGTAGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAGTGCCAAG
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-----------------------------------------------------------------------------------------ctctaggtcactaaatgatcttcatctatatattatacatttttttcttttcatctatgctttctaggttgtcattaattatctgtttaaatatttgcagAGAGTATTTTGGAGAGGTGTTGTTGAAGAGCTTTTGTGGTTTATTAGTGGTTCAACAAATGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctgttgtacatcttgatataaaagttgacatgatttattcatttggttcctagAAAGTATTTTGGCGAGGGGTAGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAGTGCCAAG
agttgac putative branch site (score: 4)
ttcattt putative PPT
atgatttattcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatgaattttggttttgggttcatatatactactgcatagtaatttcttatttgtgtgctacttatctgatgcaattgttgtttgtgtttattgcttgaaagtttattggagaagactgaagaatatctgttgtacatcttgatataaaagttgacatgatttattcatttggttcctagAAAGTATTTTGGCGAGGGGTAGTTGAAGAGCTTCTTTGGTTTATCAGTGGCTCAACAAGTGCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT