Sequence
atgc intronic sequence ATGC exonic sequencegttattttgaacttaatacctttcttgttttttagttgttcatagagttcatctgcctgacaaaatatatatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
Basic information
species | Glycine max |
transcript | GLYMA20G30980.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g08700.3 (Oryza sativa), 3'ss of exon 9
gttattttgaacttaatacctttcttgttttttagttgttcatagagttcatctgcctgacaaaatatatatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
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----gtaagctcttatgatcctgtccactgttgtaccatgtgtactttccaaatgattgctaacatgc-----tatttttcgt---cagATACTATGCAATTGCTACTCCAAGTGCTACCCAAAGGTTGCTTTTTGGTCTTCTCGAGGCACCACCATCATGGGCCCCAGATGCACTTGATGCAGCAGTA
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 8
gttattttgaacttaatacctttcttgttttttagttgttcatagagttcatctgcctgacaaaatat-atatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
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------------gtaatctccagttcactgctatgct-ttcatctacttc------cagataaaattttaaatgggttattttttcccagATATTATGCAATTGCTACACCAAGTGCTACACAGAGGTTGCTTTTTGGTCTTCTCGAAGCACCTCCATCATGGGCTCCAGATGCACTTGATGCAGCAGTA
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 9
gttattttgaacttaatacctttcttgttttttagtt-gttcatagagttcatctgcctgacaaaatatatatac----acctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
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------------------------gtaagctccagttcactgctatgcttaatccacttcaagatatttttttagtgggatcttttcctttcagATACTATGCAATTGCTACACCAAGTGCTACACAGAGGTTGCTTTTTGGTCTTCTGGAAGCACCACCATCATGGGCTCCAGATGCACTTGATGCAGCAGTA
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G22770.1 (Arabidopsis thaliana), 3'ss of exon 7
-------------------------------gttattttgaacttaatacctttcttgttttttagttgt---tcatagagttcatctgcctgacaaaatat---atatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
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gtattgtttctgggcttaccctttcaattagggtttattggtagtagtctgttgctagttttaaggttgtgcttcctcgaatccctagatcagaattgttttctcactttcctgttatactgtcagATACTATGCCATTGCAACTCCAAGTGCTACGCAGAGACTTCTTCTTGGACTCTTAGAAGCACCACCGTCGTGGGCTCCAGATGCACTTGATGCTGCTGTA
upper sequence: GLYMA20G30980.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------gttattttgaacttaatacctttcttgttttttagttgttcatagagttcatctgcctgacaaaatatatatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
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gtgaatttccatacctttctctgtgggtaactttttatggaaaacatttcctaatttattctttcttccttttatcttttttccttttatcttttttccttttttggtg---gtggggttatctggtttagCTACTATGCAATTGCTACTCCAAGTGCCACACAACGACTTCTTCTAGGACTACTGGAAGCACCACCATCATGGGCTCCAGATGCTCTTGATGCTGCAGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgttcatagagttcatctgcctgacaaaatatatatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
acctaac putative branch site (score: 2)
tgacaaaatatatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattttgaacttaatacctttcttgttttttagttgttcatagagttcatctgcctgacaaaatatatatacacctaacatttgcagATATTATGCAATTGCTACTCCAAGTGCTACACAAAGACTTCTTCTTGGACTTCTTGAAGCACCCCCATCGTGGGCTCCAGATGCACTTGATGCTGCTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT