Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcatattgacagtagagccataccatattgcccttgtgggtgcttggatactgttttgaatcttggtcaaatatacattttagtcatggcattcttgcaccccaactactcagttattcttatattttaatttagGCTACTACTCTGCAAACTGAAGATTTGCTCGACAAACTAAGTGTCTCTTTGACTGGTGAAGAACTTGATGTCATTGAAAAGCTTTATTACCAAGCAATGA
Basic information
species | Glycine max |
transcript | GLYMA10G30680.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G30680.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G078283_T01 (Zea mays), 3'ss of exon 1
gtttgtcatattgacagtagagccataccatattgcccttgtgggtgcttggatactgttttgaatcttggt-caaatatacattttagtcatggcattcttgcaccccaactactcagttattcttatattttaatttagGCTACTACTCTGCAAACTGAAGATTTGCTCGACAAACTAAGTGTCTCTTTGACTGGTGAAGAACTTGATGTCATTGAAAAGCTTTATTACCAAGCAATGA
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----------------gtatagaattatcatctttctaatatgagtgct-----actgcattttactgtagtactggctcatgcttca---atgcaattggttcatg-----tgctgaatcatctct---------cacagGACACCACACTCCAAATAGAAGAATTGCTAGACAAACTAAGTGTCTCATTAACTGGTGAGGAACTTGAGATTATTGGCAAGCTCTACCAGCAAGCTATGA
upper sequence: GLYMA10G30680.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G32470.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttgtcatattgacagtagagccataccatattgcccttgtgggtgcttggatactgttttgaatcttggtcaaatatacattttagtcatggcattcttgcaccccaactactcagttattc-ttatattttaatttagGCTACTACTCTGCAAACTGAAGATTTGCTCGACAAACTAAGTGTCTCTTTGACTGGTGAAGAACTTGATGTCATTGAAAAGCTTTATTACCAAGCAATGA
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----------------------------------------gtatgtttttgcgtaattctgttaacttttga-gagtttctagcatgatgtgtgagatgatgcatcttttataatgaatggtctgttttcctttaatatagGCATCAGCCAAGCAAACTGAAGACTTGCTTGAGAAGCTTAGTGTCTCTATGACTGGTGAAGAATTGGACATAATTGAAAAATTGTATCAACAGGCTATGA
upper sequence: GLYMA10G30680.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0159g00050.t01 (Vitis vinifera), 3'ss of exon 3
gtttgt-catattgac-agtagagccataccatattgcccttgtgggtgcttggat----actgttttgaatcttggtcaaatatacattttagtcatggcattcttgcaccccaactactcagttattcttatattttaatttagGCTACTACTCTGCAAACTGAAGATTTGCTCGACAAACTAAGTGTCTCTTTGACTGGTGAAGAACTTGATGTCATTGAAAAGCTTTATTACCAAGCAATGA
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gtttgtacttagcagtgagcatttttattttattttaaaattgtctaactgtaaatctctgctgacgccattctgagagaagtatactttacataaatggttttct--cactcaggcagcttaactaacttgttctttgaatttagGGTTCAGCTTTACAAACTGAGGACTTGCTGGATAAACTAAGTGTCTCTTTGACAGGCGAAGAGCTTGACATCATAGAAAAGCTTTATTACCAAGCTATGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagtcatggcattcttgcaccccaactactcagttattcttatattttaatttagGCTACTACTCTGCAAACTGAAGATTTGCTCGACAAACTAAGTGTCTCTTTGACTGGTGAAGAACTTGATGTCATTGAAAAGCTTTATTACCAAGCAATGA
ttttaat putative branch site (score: 3)
tactcagttattctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcatattgacagtagagccataccatattgcccttgtgggtgcttggatactgttttgaatcttggtcaaatatacattttagtcatggcattcttgcaccccaactactcagttattcttatattttaatttagGCTACTACTCTGCAAACTGAAGATTTGCTCGACAAACTAAGTGTCTCTTTGACTGGTGAAGAACTTGATGTCATTGAAAAGCTTTATTACCAAGCAATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA