Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcggggggcatacttgattaatccatatttctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatttctgcagtagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATTAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
Basic information
species | Glycine max |
transcript | GLYMA17G05410.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 9
gtaagtcggggggcatacttgatta-atccatatttctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatt-tctgcagtagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATTAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
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-------gtaagttgtactttgcaacagtaatactgtttgattctatatatgtttttttggtactttggtaatgtttcgttcacattcctgatagtctataa-atgcttcattcgcatt----aaatccccgtgagtgaaaactttgccataatgtgatg---------gtatttcatctgtcttca-----cagGAAAACATGTCTAGGATGCTGTTAGTAACAGATGTACAGGATATCATTAAAAGGCACCAGGCCCAGATTATTACCTCTTTGAAAGATCCAGATATCAG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtcggggggcatacttgattaatccatatttctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatttctgcag-tagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATTAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
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-----------------------------------------------------------------------gtgagatcttgcatacc-acttcctgcatctaagcctagctggagtagtttgtgaagtggt--tggtggt--ttctcatgatgcatttt-----ttgacaaaat--------------tacagGAAAATATGACGCGGATGCTGATGGTCACAGATGTTCAAGATATCATAAAGAAGCATCAGTCTCAGATAATCACCTCCTTGAAAGACCCTGACATCAG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagtcggggggcatacttgattaatccatatttctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatttctgcag-tagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATTAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
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-----------------------------------------------------------------------gtgagatcttgcatacccacttcctgcatctaagcttagctagaacagtaatttgttaagtatt--tggtagt--gcattatgtggcttc-----tcatgatgcttgt-tgacaacattgcagGAAAATATGACGCGAATGCTGATGGTCACAGATGTTCAAGATATCATAAAGAAGCATCAGTCTCAGATAATCACCTCGTTGAAAGACCCTGACATCAG
upper sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtcggggggcatacttgattaatccatatttctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatttctgcagtagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATTAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
| ||| ||| || || | | ||| || | || | | | | | | | |||| | || ||| | | ||| || | | || ||| || || | | |||| | |||| | | |||| || || | || ||||||| || ||||| | ||| ||||||| | ||||| || ||||| |||||||||||||| ||||| || || |||||| |||||||||||||||||||
---------gtaagttacaggatggttctatctgtg-cttccgttatgtcttcacctatatccaatgattaaa--------gcatatcaaa---ctggcatgcaccatgttagaatt-tgaatggattgatgtcattgcttgctgtctaactgcatgatt--------tgacatttagattactctgctgcagGAAAACATGACTCGGATGCTGATGGTGTCCGATGTGCAGGATATTATTAAAAGACATCAGGCTCAAATCATAACCTCACTGAAGGATCCTGACATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATTAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
tcataac putative branch site (score: 2)
ttcataacatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcggggggcatacttgattaatccatatttctcttttcttgttcttttatttctgtttgaaggagggacaaggattgcatgcccaatttctgcagtagatttcattatcatagtagaaggcttggtggtggtggtggttgtcataatgcaatgtcccagttcataacatatatgctattatggtgcagGAGAATATGACAAGAATGTTGATGGTTACTGATGTACAAGATATCATTAAAAGACATCAAGCTCAGATTATTACCTCATTGAAGGATCCTGACATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG