Sequence
atgc intronic sequence ATGC exonic sequencegcaagtataacttttttttcttctttgagggtgaggtggggtgtggataagcttcttgttttcatgatcttatctattgttttttgaattacatcatcttattatctgagccatgtttcctattttcttccaccaattttttttatatctcacaaattaacaatttagtgctttggctccatggttatcatgatcagATCGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGATGTGGTCCCTTGGTGGATTTGTGTCGTGGGCCCCATATACCTAATACAT
Basic information
species | Glycine max |
transcript | GLYMA01G03930.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G26830.1 (Arabidopsis thaliana), 3'ss of exon 5
gcaagtataacttttttttcttctttgagggtgaggtggggtgtggataagcttcttgttttcatgatcttatctattgttttttgaattacatcatcttattatctgagccatgtt-tcctattttcttccaccaattttttttatatctcacaaattaacaatttagtgctttggctccatggtta-tcatgatcagATCGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGATGTGGTCCCTTGGTGGATTTGTGTCGTGGGCCCCATATACCTAATACAT
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------------------------------------------------------------------------------gtgggttaagctgtgtataaatatcat-tggattgtgttatgctcacctaaccttacattcatttctgtcctctatgaagttgttgtttggactcattattctgctgttaatcatg--tagGTTGAACTCATCAATGGTTTGCCTGCAGACATGACCATTACTGTCTACAGATGTGGCCCTTTGGTGGATTTGTGTCGTGGACCGCACATACCAAATACTT
upper sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0015g00470.t01 (Vitis vinifera), 3'ss of exon 5
gcaagtataacttttttttcttctttgagggtgaggtggggtgtggataagcttcttgttttcatgatcttatctattgttttttgaattacatcatcttattatctgagccatgtttcctattttcttccaccaattt-tttttatatctcacaaattaacaatttagtgctttggctccatggt-tatcatgatcagATCGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGATGTGGTCCCTTGGTGGATTTGTGTCGTGGGCCCCATATACCTAATACAT
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------------------------------------------------------------------------------gtgagtgaagctccatttttatatcatccataccatttgagctatccttagctacttccttattttcttactactcttattgttactcatatgggttg--tttatcatatctcataatcagATTGAAATCATCAATGACTTACCCGAAGACAAAACTATCACAGTATACAGATGTGGGCCATTGGTTGATCTGTGCCGTGGACCCCATATACCAAATACAT
upper sequence: GLYMA01G03930.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 3'ss of exon 5
gcaagtataacttttttttcttctttgagggtgaggtggggtgtggataagcttcttgttttcatgatcttatctattgttttttgaattacatcatcttattatctgagccatgtt-tcctattttcttccaccaattt-tttttatatctcacaaattaacaatttagtgctttggctccatggttatcatgatcagATCGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGATGTGGTCCCTTGGTGGATTTGTGTCGTGGGCCCCATATACCTAATACAT
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------------------------------------------------------------------------------gtaagtgaagctccatttttatatcatccacaccatttgaccccatccttagccacttccttattttcttactattctgatcctcactcatatgggttgtttat-catctcccttaatcagATTGAAATCATCAATGACTTACCTGAAGACAAAACTATCACAGTATACAGATGTGGGCCATTGGTTGATCTGTGCCGTGGGCCCCATATACCAAATACAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatatctcacaaattaacaatttagtgctttggctccatggttatcatgatcagATCGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGATGTGGTCCCTTGGTGGATTTGTGTCGTGGGCCCCATATACCTAATACAT
aattaac putative branch site (score: 2)
acaaattaacaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtataacttttttttcttctttgagggtgaggtggggtgtggataagcttcttgttttcatgatcttatctattgttttttgaattacatcatcttattatctgagccatgtttcctattttcttccaccaattttttttatatctcacaaattaacaatttagtgctttggctccatggttatcatgatcagATCGAGATTATCAATGATTTGCCTGCCGACAAAACTATCACAGTATACAGATGTGGTCCCTTGGTGGATTTGTGTCGTGGGCCCCATATACCTAATACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA