Sequence
atgc intronic sequence ATGC exonic sequencegtaacagtctgctgtaaagtgatttctgccttcacaagaaattcatttacaaaaaaaaattagttgaagattgaaaacatacaggaaaacaaacggcagggcattatcttctgttgaacaaactgagatcaaatatctgtttctttgaaatactacaaagtgctcttctgataattttaataaatgaatgcagGGCCATGAACCATTTGTTTCATATGAGGGTCTTGAGCAGCTGCATCGGTTCTTATTTGTTCTTGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
Basic information
species | Glycine max |
transcript | GLYMA08G20120.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os11g07912.1 (Oryza sativa), 3'ss of exon 3
gtaacagtctgctgtaaagtgatttctgccttcacaagaaattcatttacaaaaaaaaattagttgaagattgaaaacatacaggaaaacaaacggcagggcattatcttctgttgaacaaactgagatcaaatatctgtttctttgaaatactacaaagtgctcttctgataattttaataaatgaatgcagGGCCATGAACCATTTGTTTCATATGAGGGTCTTGAGCAGCTGCATCGGTTCTTATTTGTTCTTGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
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----------------------------------------------------------------------------------------gtagtcggtctggttctat--tccatccaaggatggtcgattggacgttcgaggcatggcactttttggtgat--tcagctggtgttttctct----gcttgcagGGTCATGAGCCTTTTGTTTCATATGAAGGCCTTGAACAGCTGCATCGGTTCTTGTTTATCCTTGGTATCACCCATGTGTTGTACACTTTTGTAACTGTTG
upper sequence: GLYMA08G20120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G089259_T01 (Zea mays), 3'ss of exon 3
gtaacagtctgctgtaaagtgatttctgccttcacaagaaattcatttacaaaaaaaaattagttgaagattgaaaacatacaggaaaacaaacggcagggcattatcttctgttgaacaaactgagatcaaatatctgtttctttgaaatactacaaagtgctcttctgataattttaataaatgaatgcagGGCCATGAACCATTTGTTTCATATGAGGGTCTTGAGCAGCTGCATCGGTTCTTATTTGTTCTTGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
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------------------------------------------------------------------------------gtattggtaacccagatgtcctgc-tcccagcctattgaggtcaatggaactgggagcggagcacactgt----tcactcatcgcttgggttggaacctaatctgtcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG
upper sequence: GLYMA08G20120.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g00260.t01 (Vitis vinifera), 3'ss of exon 3
gtaacagtctgctgtaaagtgatttctgccttcacaagaaattcatttacaaaaaaaaattagttgaagattgaaaacatacaggaaaacaaacggcagggcattatcttctgttgaacaaactgagatcaaatatctgtttctttgaaatactacaaagtgctcttctgataattttaataaatgaatgcagGGCCATGAACCATTTGTTTCATATGAGGGTCTTGAGCAGCTGCATCGGTTCTTATTTGTTCTTGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
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--------------------------------------------------------------------------------------------------gtaaatccttctattcctgttacattatgttggggttttgatttggtgaaggaacta-gtagtact----aaaagtcgtcgataatggattgcagGGCCGTGTACCGTTTGTTTCCCAAGAAGGTCTAGAGCAGCTTCACCGGTTTCTGTTTGTTCTTGGCATTACCCATGTCGTGTATAGTTGTATGGCGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttctttgaaatactacaaagtgctcttctgataattttaataaatgaatgcagGGCCATGAACCATTTGTTTCATATGAGGGTCTTGAGCAGCTGCATCGGTTCTTATTTGTTCTTGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
ttttaat putative branch site (score: 3)
ttctgataattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacagtctgctgtaaagtgatttctgccttcacaagaaattcatttacaaaaaaaaattagttgaagattgaaaacatacaggaaaacaaacggcagggcattatcttctgttgaacaaactgagatcaaatatctgtttctttgaaatactacaaagtgctcttctgataattttaataaatgaatgcagGGCCATGAACCATTTGTTTCATATGAGGGTCTTGAGCAGCTGCATCGGTTCTTATTTGTTCTTGGGATCACTCATGTTCTGTATAGTTGTCTGGCTGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT