Sequence
atgc intronic sequence ATGC exonic sequencegtaagttacctctttttgcatgtatttatttctttaattagtttccaaaattacatcttatatgcatctaacgaaagtttctttatgaattaacaatgcaacacatctataaagttgtttgcttttttgtgtaattttcctgcaatggttatcaagtttaatgtttcctgtgacagAAAGACGACCTCAAGATGGTGGTGTCACATTTAAAAAGCAACAAACTAGTATCTCATATTGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG
Basic information
species | Glycine max |
transcript | GLYMA15G12950.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g40730.1 (Oryza sativa), 3'ss of exon 4
gtaagttacctctttttgcatgtatttatttctttaattagtttccaaaattacatcttatatgcatctaacgaaagtttctttatgaattaacaatgcaacacatctataaagttgtttgcttttttgtgtaattttcctgcaatggttatcaagtttaatgtttcctgtgacagAAAGACGACCTCAAGATGGTGGTGTCACATTTAAAAAGCAACAAACTAGTATCTCATATTGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG
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------------------------------------------------------------------------------------gtacatagtcatcataattt-tttgaaaacacactcttattgttttgcaattgcactaatctgataa--aaatacaatcactct-----cagAAACAGGATCTCAAATGCGCGGTGTCCTTTTTGCGAAACAATAAGGAAGTTTCTTGCATAGGCCTTTGGGGGCGATCAATGGGTGCTGTTACAAG
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G092895_T01 (Zea mays), 3'ss of exon 4
gtaagttacctctttttgcatgtatttatttctttaattagtttccaaaattacatcttatatgcatctaacgaaagtttctttatgaattaacaatgcaacacatctataaagttgtttgcttttttgtgtaattt-tcctgcaatggttatcaagtttaatgtttcctgtgacagAAAGACGACCTCAAGATGGTGGTGTCACATTTAAAAAGCAACAAACTAGTATCTCATATTGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG
| | | || || | | | | | | | || |||| | ||||| || | | | | | | | || |||| | || ||||| | ||||| | | | || || | ||| ||| ||| |||||||||||||| ||||||||||||||||| ||
----------------------------------------------------------------------------------gtgcgtacacactataaattttgtagcaacattcatattctattttaaatggcaagtcctgaaaaatattaccactgtggtactccc------agAAGCAGGATCTCAAATGTGCTGTGTCCTTTCTGCGTAAGAATAAGCAAGTTTCTTGTATAGGTCTTTGGGGACGCTCAATGGGTGCTGTTACAAG
upper sequence: GLYMA15G12950.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G17150.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttacctctttttgcatgtatttatttctttaattagtttccaaaattacatcttatatgcatctaacgaaagtttctttatgaattaacaatgcaacacatctataaagttgtttgcttttttgtgtaattttcctgcaatggttatcaagtttaatgtttcctgtgacagAAAGACGACCTCAAGATGGTGGTGTCACATTTAAAAAGCAACAAACTAGTATCTCATATTGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG
|| || | | || | || ||| || | |||| || || | | || || || || | | | |||| || || ||||||| ||||| || | | | || || ||| | |||||| | |||||| |||||||||||||| |||||||| ||||| ||
------------------------------------------------------------------------------------gtgtgttttcgg-gtcttactttctcaaggttcttcgtcttttc------cttatctaaatt--ttttcttcttaaa-----cttaagctagAAGGATGATCTCAAGACTGTGGTATCTTACCTGAGAAACAGCAATCAAGTATCCCGTATTGGACTTTGGGGACGATCTATGGGTGCAGTTACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttttgtgtaattttcctgcaatggttatcaagtttaatgtttcctgtgacagAAAGACGACCTCAAGATGGTGGTGTCACATTTAAAAAGCAACAAACTAGTATCTCATATTGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG
gtttaat putative branch site (score: 4)
tgtttcct CT-rich tract
ttatcaagtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttacctctttttgcatgtatttatttctttaattagtttccaaaattacatcttatatgcatctaacgaaagtttctttatgaattaacaatgcaacacatctataaagttgtttgcttttttgtgtaattttcctgcaatggttatcaagtttaatgtttcctgtgacagAAAGACGACCTCAAGATGGTGGTGTCACATTTAAAAAGCAACAAACTAGTATCTCATATTGGTCTTTGGGGACGATCAATGGGTGCTGTTACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT