Sequence
atgc intronic sequence ATGC exonic sequencegtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
Basic information
species | Glycine max |
transcript | GLYMA10G31880.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 6
gtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaataaataatttgtaata---ttgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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-------------------------------------------------gtaagtattttgtcttatcaggtattgaaaaatctcttggagtacaacaccattttacaatgcatctgttttcagGCATTCGATCAGCAGCAACAAGATTTGGTTGATGCTGCATCAAAAGCTTTATCCTACAGACAAGACATTATTGAAGAAAATATCCGTCTGACATATGCCT
upper sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
gtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaat-aaataatttgtaatattg----ctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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--------------------------------------gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
upper sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 5
gtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaataaataatttgtaatattgct-----gctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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----gtaaacattttatttatgacgcatcaagtactaccttggagtttgtaaaaaa--aaactactaccttagagtcatggcactatgatttaagtgtttatttttttcctttttttgtggggcagGCATTTGATCAGCAGCAGCAAGATCTGGTTGATGCTGCATCGAAAGCTTTGTCCTACAGACAGGATATTATCGAAGAAAACATCCGTCTTACATATGCAT
upper sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
gtatgcatgaaattttgtcaaagtct-ttgtgaaattccttaagcatcttttatgttttgcacttttcct-tttatttgattgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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------gttagcttttctttttatctattacaaaatatgtgtaac-tttatcttgtgacgaattatagttacttattctgttaaccacttagg-gggtaatttatctttcttgttg-tgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
upper sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G23490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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----------------gtaggcctttccttttttttacttatctgttttattcatctcgta---ttaaatgtatttaatttaattgtttggaagctgaaagattgttgctgttgtaaccagGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCAAAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttatttgattgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
atttgat putative branch site (score: 5)
tcaaataaataatttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA