Sequence
atgc intronic sequence ATGC exonic sequencegttgtttggaattcatttgctttatcattttttctctgttattattgaattgaataaatattttacactttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG
Basic information
species | Glycine max |
transcript | GLYMA03G18730.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g08000.1 (Oryza sativa), 3'ss of exon 2
gttgtttggaattcatttgctttatcattttttctctgttattattgaattgaataaatattttacactttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG
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----------------------------------------gttattgg-ctgttaaaataattgatcatttcta-tcttgctatatcgtgcagaaataacc--taacatttttattatattagGCTCTTGTTGTGCTTGTACATGATATGGGTCAAAACTGGGAACTGGTTAGTGACGCACTGAACAGCATTGTTCAATTGAAG
upper sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G24870.1 (Arabidopsis thaliana), 3'ss of exon 15
gttgtttggaattcatttgctttatcattttttctctgttattattgaattgaataaatattttacactttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG
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--------------------------gttttttattcgtcatctttcattaacatcgatgtactg-----------ttggttgctttatgagtatctaatttattttttcctacc--atatagGCGCTTGTTGTCCTGGTGCATGATATGGGGCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
upper sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G24880.1 (Arabidopsis thaliana), 3'ss of exon 14
gttgtttggaattcatttgctttatcattttttctctgttattattgaattgaataaatattttacactttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG
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--------------------------gttttttattcgtcatctttcattaacatcgatgt-----actgttggttgcttta--tgagtatctaatttatc----tttttctacca--tatagGCGCTTGTTGTCCTGGTGCATGATATGGGCCCTAACTGGGAGCTCATTAGTGATGCAATGAACAGCACTCTTAAAATTAAG
upper sequence: GLYMA03G18730.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0005g06680.t01 (Vitis vinifera), 3'ss of exon 15
gttgtttggaattcatttgctttatcattttttctctgttattattgaattgaataaatattttacactttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG
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-----------------------gttattcttcctttttctttttctgatgttgtcttttttattcttagtgatagaaagtaaaagtgctgaagttttactagtgttat------tattatagGCACTTGTGGTCCTTGTACATGATATGGGTGCAAATTGGGAGCTTGTAAGTGATGCTATCAACAGCACTCTCCAATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG
ggcttac putative branch site (score: 3)
ttattctcctgcct putative PPT
tatcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtttggaattcatttgctttatcattttttctctgttattattgaattgaataaatattttacactttaaaatctatcaattgtgtaaagggcttaccattattctcctgcctgttgcagGCTCTTGTGGTGCTGGTGCATGATATGGGTCCAAACTGGGAGCTCGTAAGTGATGCTATCAATAGTGCTCTCCAAATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT