Sequence
atgc intronic sequence ATGC exonic sequencegtatcttaccatatatattgaaacatcttttgattttgcttttaaaacatcaaatatttttctctgagccaaaagagatcttggaaaagtgcaatttggatctcctagatcttgtgcacaacttttaacttttataatgatttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG
Basic information
species | Glycine max |
transcript | GLYMA20G38200.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 13
gtatcttaccatatatattgaaacatcttttgattttgcttttaaaacatcaaatatttttctctgagccaaaagagatcttggaaaagtgcaatttggatctcctagatcttgtgcacaacttttaacttttataatgatttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG
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----------------------------------------gtagagaggcctgaattaattttccactctat------ttgtttaatattgtcctgttaccttcctaggtcatgga------ttaagattagtataatgtt-----agtttctttcttttccttcttttgctaacagtctgaattttg---cagATATATGTGCACAGTAAGTTGATGATCATTGATGACCGGATGACACTGATTGGATCAGCTAACATAAATGACAGAAGTTTGCTTGGATCAAGGGATTCTG
upper sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 14
gtatcttaccatatatattgaaacatcttttgattttgcttttaaaacatcaaatatttttctctgagccaaaagagatcttggaaaagtgcaatt-tggatc-tcctagatcttgtgcacaacttttaacttttataatgatttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG
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------------------------------------------------------------------------gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcacttt--gccatttaagagtt---gtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
upper sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G158008_T01 (Zea mays), 3'ss of exon 5
gtatcttaccatatatattgaaacatcttttgattttgcttttaaaacatcaaatatttttctctgagccaaaagagatcttggaaaagtgcaatttggatctcctagatcttgtgcacaacttttaacttttataatgatttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG
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-----------------------------------------------------gtacttttttttgtt--------ggtggtggtagggtgggggtcaaaatgcttctgttacactcaataggtcatgcctttaggcaaggttagtttctgtgcttcttttatttttttcctaacaatttgcatgttg---cagATATATGTGCACAGTAAATTGATGATTATTGATGATCGCATGGCATTGATTGGCTCAGCCAACATAAATGATAGAAGCTTGCTTGGATCTAGGGATTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG
tattgat putative branch site (score: 3)
aaatatttgtcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttaccatatatattgaaacatcttttgattttgcttttaaaacatcaaatatttttctctgagccaaaagagatcttggaaaagtgcaatttggatctcctagatcttgtgcacaacttttaacttttataatgatttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA