Sequence
atgc intronic sequence ATGC exonic sequencegtttgtaaatttaggaatatttttgaatgctactcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
Basic information
species | Glycine max |
transcript | GLYMA12G30520.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 6
gtttgtaaatttaggaatatttttgaatgctactcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
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-----------------------------ctggtttgttcaaagaaatatatgcgtctgttgtggccattggatttgtattttctatatgtctc----caactgtttttcaagcttaa-attttctatatac---agGTTAAGACAATGAGGGCTCTTCAGTACTTCCCTACAATTGAAGATCCTGGCGCAAGACGAGCTTTATTTGAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 6
gtttgtaaatttaggaatatttttgaatgctactcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
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--------------------------------attttacatctttgattttatgttggcgtgtgaagg--aaaccatgtatatgcat-tggatggaacca--tgtattcagctaagaataaaatttaattttcacagGTTAAGACAATGAGAGCTCTTCAGTACTTCCCTACCATTGAAGATCCCAACGCAAGACGGGCTTTGTTTGAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 7
gtttgtaaatttaggaatatttttgaatgctactcttaccagcttgcttttattgagaac---caaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
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-----------------------------ttggttctatgttggtgtgttgaaggaaaacatacatgcacattggatggaaatggtccatgttt------tcaactaagaataacatttta-----ttttcacatcacagGTTAAGACAATGAGAGCTCTTCAGTACTTCCCTACCATTGAAGATCCCAACGCAAGACGAGCTTTGTTTGAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 6
-----------------------gtttgtaaatttaggaatatttttgaatgctactcttaccagctt---gcttttattgagaaccaaaaatgttgaactaaattttttctta---tccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
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gtttgtcttaactcggttaatacgttcaatattttttaatcacatccttttcccaatctcatgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttgccccagctttggtatgttgtggttgttggatacttatatatctttggc-agtacagGTTAAGGCAATGAGGGCTCTTCAATATTTTCCAACCATTGAAGATCCCAGTACCAGAAAAGCTCTCTTTGAG
upper sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------------------------------------------------gtttgtaaatttaggaatatttttgaatgctac-tcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
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gtttgacttaactcggcttattcactcttgtttaatagcttaaatattctttaatcgcatccttttcacaaatcctgtgcattttaaacattttatgtgaaattagcttatgaaaatagaggcttggcccagctttggtgtatttttg-ttactcagttaa--agatatcgtggatacttatatatctttggttagtacagGTTAAGGCAATGAGGGCTCTTCAATATTTCCCGACCATTGAAGATCCCAGTACCAGAAAAGCTCTGTTTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
tgcttac putative branch site (score: 2)
tttttgctt CT-rich tract
ttttttagtgtttaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtaaatttaggaatatttttgaatgctactcttaccagcttgcttttattgagaaccaaaaatgttgaactaaattttttcttatccagcaagttaaccttttttagtgtttaacaatttttgcttactgtagGTGAAAACAATGAGGGCTCTTCAATATTTTCCTACCATTGAAGATCCTAATGCCAGAAGGTCATTGTTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA