Sequence
atgc intronic sequence ATGC exonic sequencegtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
Basic information
species | Glycine max |
transcript | GLYMA20G34250.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G04500.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
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------------------------------------------------gtctttgtgcttaaccat----cataaccggat-taaaccagtggttatccatatac--cgatttgtt--cacatgttttt---tttgttatattttgt---------tgtagTATGCATGTAGGAAGACGTTGGCAGATAGTCGTCCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAACCAAATAGACAAGCCTGTTCAA
upper sequence: GLYMA20G34250.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G33350.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttat-aaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaata--tgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
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----------------------------------------------------------------------------------------gttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGATTTGCAAAGAATGATGAATTTGGTGAGCCAAATAGACAAGCTTTTTCAA
upper sequence: GLYMA20G34250.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv05s0049g01830.t01 (Vitis vinifera), 3'ss of exon 3
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcat-atgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
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--------------------------------gttatctctctctctctcgttcttctgctatcattttacattcagatcatgtatagg----catacgtatgataacttaaactttattttcttactaaatgttagaaaaat-ataataataataatgcagTATGCATGTCGCAAGACACTGGCAGACAGCAGACCACGAGTTAGAGGAAGATTTGCCAAAAATGATGACTTTGGAGAGGCCCCTAGAGCCAGTGGTGGAC
upper sequence: GLYMA20G34250.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S143_20V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTA-GCA
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-------------------------------------------------tatctgattctca--gtagagcaactgcatgagaaggtgattattt--cagtgggtgccgagctctaatcgt----ttttga---ctgtttttttcgcaatattgt-ttcagTATGCCTGTCGCAAAACATTGGCAGATAGTCGACCTCGAGTTCGAGGGCGTTTTGCAAAGAAC-ATGGATGATGATTTACCGACCGCTCTCCTAGGGCGCA
upper sequence: GLYMA20G34250.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S70_278V6.1 (Physcomitrella patens), 3'ss of exon 4
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
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-------------------------------------------------gatttag-tctccccaagtagagcagctgaatacgacat-tgcatttagtgagtactagggcctgaccgtgtttacct----gatc------tggtgcaatgccttttccagTACGCCTGCCGGAAAACTTTGGCAGATAGCCGCCCACGAGTTCGAGGACGTTTTGCAAAGAACATGGATGATGATCTACCGACCGCTGCCTTTGGGCGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
aactaat putative branch site (score: 2)
ttgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcagTATGCCTGCCGCAAAACTCTGGCAGATAGCCGACCTCGAGTTAGAGGAAGGTTTGCAAAGAATGATGACTTTGGAGAAACCAATAGAACTACTAGTAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
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