Sequence
atgc intronic sequence ATGC exonic sequencegtatgttgacctgcaaattatgtactgtaacttggtagtgaatcaattgatctattgaacatatgccaatcaattcattgttcttgtataccttctatgaaacctttcagaatttgtatttcctcagatgctagaggatgcttacaccatctaatcctaatatggttgattttatcttaactcttcagCATATTTGTGGCAATTGATGCGATACAACATCCTTCAACTTCTAAAGAACCTGAGATTTCACTCTCATGGGAAGGAAATAATTGATGCTGATATTCTGCG
Basic information
species | Glycine max |
transcript | GLYMA08G45800.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G45800.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G081380_T02 (Zea mays), 3'ss of exon 9
gtatgttgacctgcaaattatgtactgtaacttggtagtgaatcaattgatctattgaacatatgccaatcaattcattgttcttgtataccttctatgaaacctttcagaatttgtatttcctcagatgctagaggatgcttacaccatctaatcctaatatggttgattttatcttaactcttcagCATATTTGTGGCAATTGATGCGATACAACATCCTTCAACTTCTAAAGAACCTGAGATTTCACTCTCATGGGAAGGAAATAATTGATGCTGATATTCTGCG
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---------------------------------------------------------------------ttcaaacgttctttttat-tatatgccatggatggttagttggtttgctcctcttttgcaacttctgg----taggaccatataat------gaaattgcatttatcctagCTTTTC--------TATGGCAATTGATGCGGTACAACATTCTACAACTGCTGAAGAATCTTAGATTTCACTCAAATGGAAAAGAGATCACAGATAATGACATATTGGC
upper sequence: GLYMA08G45800.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G48460.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgttgacctgcaaattatgtactgtaacttggtagtgaatcaattgatctattgaacatatgccaatcaattcattgttcttgtataccttctatgaaacctttcagaatttgtatttcctcagatgctagaggatgcttacaccatctaatcctaatatggttgattttatcttaactcttcagCATATTTGTGGCAATTGATGCGATACAACATCCTTCAACTTCTAAAGAACCTGAGATTTCACTCTCATGGGAAGGAAATAATTGATGCTGATATTCTGCG
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---------------------------------------------------------------------------------------------------------gtaaaaatttctcaactctataattgt-gtgtttttatgaatcaccaactttaataatgagttgttttgaaaccatcttccagCATACTTATGGCAATTGATGAGATACAACATCCTGCAACTTCTTAAGAACTTGAGACTACATTCAAACGGCAAAGAGATAACAGACGCTGATATATTGGA
upper sequence: GLYMA08G45800.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 3'ss of exon 8
gtatgttgacctgcaaattatgtactgtaacttggtagtgaatcaattgatctattgaacatatgccaatcaattcattgttcttgtataccttctatgaaacctttcagaatttgtatttcctcagatgctagaggatgcttacaccatctaatcctaatatggttgattttatcttaactcttcagCATATTTGTGGCAATTGATGCGATACAACATCCTTCAACTTCTAAAGAACCTGAGATTTCACTCTCATGGGAAGGAAATAATTGATGCTGATATTCTGCG
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------------------------------------------------------------------------------------------------gtatgttgtctaacatttctttttcccctatatattagataccaacttgattacctgaacaaaaaatg-------ttggccttgctcttcagCTTATTTATGGCAATTGATGCGATTCAACATCCTCCAACTTCTAAAGAACTTGAGGTTTCATTCCCATGGGAAGGAAATCATTGATGCTGATATTCTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaggatgcttacaccatctaatcctaatatggttgattttatcttaactcttcagCATATTTGTGGCAATTGATGCGATACAACATCCTTCAACTTCTAAAGAACCTGAGATTTCACTCTCATGGGAAGGAAATAATTGATGCTGATATTCTGCG
tcttaac putative branch site (score: 2)
ctcttc CT-rich tract
ttgattttatcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttgacctgcaaattatgtactgtaacttggtagtgaatcaattgatctattgaacatatgccaatcaattcattgttcttgtataccttctatgaaacctttcagaatttgtatttcctcagatgctagaggatgcttacaccatctaatcctaatatggttgattttatcttaactcttcagCATATTTGTGGCAATTGATGCGATACAACATCCTTCAACTTCTAAAGAACCTGAGATTTCACTCTCATGGGAAGGAAATAATTGATGCTGATATTCTGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT