Sequence
atgc intronic sequence ATGC exonic sequencegtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
Basic information
species | Glycine max |
transcript | GLYMA20G35770.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g01060.2 (Oryza sativa), 3'ss of exon 6
gtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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------------------------------------------gtaagtattttgtcttatcaggtattgaaaaatctcttggagtacaacaccattttacaatgcat----ctgttttcagGCATTCGATCAGCAGCAACAAGATTTGGTTGATGCTGCATCAAAAGCTTTATCCTACAGACAAGACATTATTGAAGAAAATATCCGTCTGACATATGCCT
upper sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
gtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaat-aaataatttgtaatattg----ctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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--------------------------------------gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
upper sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G104377_T03 (Zea mays), 3'ss of exon 5
gtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaataaataatttgtaatattgct-----gctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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----gtaaacattttatttatgacgcatcaagtactaccttggagtttgtaaaaaaaaac-tactaccttagagtca-tggcactatgatttaagtgtttatttttttcctttttttgtggggcagGCATTTGATCAGCAGCAGCAAGATCTGGTTGATGCTGCATCGAAAGCTTTGTCCTACAGACAGGATATTATCGAAGAAAACATCCGTCTTACATATGCAT
upper sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
gtatgcatgaaattttgttgaaatct-ttgtgaaattccttaagcatcttttgtgttttgcatttttcct-tatatttggttgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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------gttagcttttctttttatctattacaaaatatgtgtaac-tttatcttgtgacgaattatagttacttattctgttaaccacttagg-gggtaatttatctttcttgttg-tgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT
upper sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G23490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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----------------gtaggcctttccttttttttacttatctgttttattcatctcgtattaa---atgtatttaatttaattgtttggaagctgaaagattgttgctgttgtaaccagGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCAAAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttatatttggttgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaataaataatttgtaatattgctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA