Sequence
atgc intronic sequence ATGC exonic sequencegtattccttgttagtgtaacctttttgtatttttattttattttattgaatctgaatttagcagacatgttctttggtttgatttttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT
Basic information
species | Glycine max |
transcript | GLYMA14G10950.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g39260.1 (Oryza sativa), 3'ss of exon 4
gtattccttgttagtgtaacctttttgtatttttattttattttattgaatctgaatttagcagacatgttctttggtttgatttttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT
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------gtttgaattctgaaagatctgaatggctaattc--cttgttta--ctgaacttattcc-tgtgtagttctgattgataaaatatgtgt---agGCCTTGGTCTAAATGAAGAGGTTCAACCAAGCATGGAATCTAATACGAAATTCAGTGATGTAAAGGGTGTCGATGAAGCCAAAGCTGAACTTGAGGAAAT
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G096764_T01 (Zea mays), 3'ss of exon 4
gtattccttgttagtgtaacctttttgtatt-tttattttattttattgaatctgaatttagcagacatgttctttggtttgatttttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT
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-------------gtttgatttttgtgaaagatatgtattatctt-ttgaacggcaagtcagcccattaacccttta--tagattgaatgta-------gGTCTTGGTCTGAATGAAGAGGTTCAACCAAGCATAGAGTCTACTACAAAATTCAGTGATGTAAAGGGTGTTGATGAAGCAAAATCTGAACTTGAAGAAAT
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G26140.1 (Arabidopsis thaliana), 3'ss of exon 4
gtattccttgttagtgtaacctttttgtatttttattttattttattgaatctgaatttagcagacatgttctt-tggtttgatttttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT
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-------------gtagagtttggttgtgttttc-ttcagtgatccaatagctgtattgaatgactttgtgctcattaatttatgcttaatacatgttagGACTTGGTTTGCACGAAGAAGTGCAACCTAGTATGGATTCGAGCACCAAATTTTCTGATGTAAAGGGTGTTGATGAAGCAAAGGCTGAGCTAGAGGAAAT
upper sequence: GLYMA14G10950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0008g01170.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------gtattccttgttagtg-----taacctttttgtatttttattttattttattgaatctgaatttagcagacatgttctttggtt--------tgatt-tttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT
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gtatttgtcttgatacttcaggtgctaccctctgaatacgattttatgccagatgaaacaacactaccctacgcctatcctcatcctctccccccaaacaaacatccccaccctctcttctttctctctctcatgtggttgttttccatgtttcagGACTTGGTCTAAATGAAGAGGTGCAACCTAGCATGGAATCAAATACAAAATTTAATGATGTAAAGGGTGTTGATGAGGCAAAAGCTGAGCTAGAAGAAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaatctgaatttagcagacatgttctttggtttgatttttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT
gtttgat putative branch site (score: 5)
tttttcatatttccc CT-rich tract
tttgatttttcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattccttgttagtgtaacctttttgtatttttattttattttattgaatctgaatttagcagacatgttctttggtttgatttttcatatttcccagGACTTGGTATAAATGAAGAAGTGCAACCTAGCATGGAATCAAGTACAAAATTTAGTGATGTAAAAGGTGTCGATGAGGCAAAGGAAGAGCTGGAAGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA