Sequence
atgc intronic sequence ATGC exonic sequencegtacaaaccaattacctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
Basic information
species | Glycine max |
transcript | GLYMA18G18510.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
gtacaaaccaattacctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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----------------------ctgtgttgtattatttgataggtctgcatttg--taagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatt---tgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
upper sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 3
gtacaaaccaattacctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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-------------------------gtctgtaa---tcaaacactgtatttatacactcacgtcagggaccatatgctctgtggaacttttttaccatt-------tgggctct---tgttgtacagGTTGATCGGGTCTTGTACTCGTCAGTGGTTTACCCCCACAACTACGGCTTCATCCCTCGAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGC
upper sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacaaaccaattacctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccataccca--tctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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---------------------------------------gttagatgagaacaaagtttattttttatatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattct--ctcattc--agGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCA
upper sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 2
gtacaaaccaattacctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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--------------------------------------------------------------gtgtgaatagtttgatcttttctttcg--cta-ctttccagttatgctttggtcgttcttc-cagGTTGATCGAGTCCTTTATTCCTCGGTGGTTTATCCACACAACTATGGATTTGTTCCACGCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttcccccatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
tgcttac putative branch site (score: 2)
atttctgaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaaccaattacctggttactggaatggaagcccctactgctatatcttgaaacaaattttccagatgattttttcccccatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCATTTGTTTATCCATATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA