Sequence
atgc intronic sequence ATGC exonic sequencegttggtgtctttgtcttcctattctatctaagagttattattttaattttatttcattattttgagctccatatgaacgtggctgtgtttttaattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
Basic information
species | Glycine max |
transcript | GLYMA20G38450.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38450.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 5
gttggtgtctttgtcttcctattctatctaagagttattattttaattttatttcattattttgagctccatatgaacgtggctgtgtttttaattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
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---------------------gtcagtgcaaatgcattcattttc-ttctgttttactgtat--ggttgcttct-aacttctttatttggtgcatacagAGCATGAATCGCATGGCTCATTTGAAACGAGCCGAGTATGGGAAAGTTGATTTGGATTACGTGCTTGGAATTGGAGGCTTTGATTTGGAGAG
upper sequence: GLYMA20G38450.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G180418_T03 (Zea mays), 3'ss of exon 10
gttggtgtctttgtcttcctattctatctaagagttattattttaattt--tatttcattattttgagctccatatgaacgtggctgtgtttttaattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG--------
| || ||| || | | | |||| ||||| | || | | || | | | ||| | ||| || ||| | |||| || || ||||| | |||||||| |||||| | ||||| ||||||||||| ||||| || |||||| |||||||
---------------------------gttagtgttgcgtattcattctgctattgcattaccataagtttct----aatatcctcatttgcttagtacagGGTATCAACCACATGGCTAATTTGAAGCGAGCTGAGTATGGTAAAGTTGATTTGGACTATGTTCTTGGAATTGGAGGATTTGATCTGGAGAGGTTCCTTT
upper sequence: GLYMA20G38450.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G180418_T01 (Zea mays), 3'ss of exon 10
gttggtgtctttgtcttcctattctatctaagagttattattttaattt--tatttcattattttgagctccatatgaacgtggctgtgtttttaattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
| || ||| || | | | |||| ||||| | || | | || | | | ||| | ||| || ||| | |||| || || ||||| | |||||||| |||||| | ||||| ||||||||||| ||||| || |||||| |||||||
---------------------------gttagtgttgcgtattcattctgctattgcattaccataagtttct----aatatcctcatttgcttagtacagGGTATCAACCACATGGCTAATTTGAAGCGAGCTGAGTATGGTAAAGTTGATTTGGACTATGTTCTTGGAATTGGAGGATTTGATCTGGAGAG
upper sequence: GLYMA20G38450.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 5
gttggtgtctttgtcttcctattctatctaagagttattattttaattttatttcattattttgagctccatatgaacgtg-gctgtgtttttaattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
|| ||| ||| ||||| ||||| ||| || | ||| || | || | | || || | | | | | | |||| || | | |||| ||||||||| |||| || | ||||||||| ||||||| || ||| ||||||||||||||||||| ||||| || |||||| | || ||
gtaggt-tctgcttcttctgattctttct---tttttctctttgaacatctatttttctctgtgcactgcgttagcatttatgatgtggttatt-tccagACCATAAACAGCATGGCTCACATGAAGCGGACAAAGTATGGGAAGGTTGACTTGGATTATGTTCTTGGAATTGGAGGGTTTGATCTAGAAAG
upper sequence: GLYMA20G38450.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g08260.t01 (Vitis vinifera), 3'ss of exon 5
gttggtgtctttgtcttcctattctatctaagagttattattttaatt-ttatttcattattt-tgagctccatatgaacgtggctgtgttttt-aattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
|| | ||| || | | | | | | ||||| || || |||| || | || | | | |||| | || | || ||||| ||||| ||||||| | | ||||||||||||| |||||||||| ||||||||||||| ||||| | || |||||||||||||||||
------gttggtaccttgcttcttgcttggatggctttcatttttcttattgtttcgttttggatgtgttggactgtggtgtggtacttttgctgaaagcagAATATAAATCGCTTGGCTCATCTCAAGCGGACAGAGTTTGGAAAAGTTGACTTGGATTATGTACTTGGAGTAGGAGGCTTTGATTTGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttatttcattattttgagctccatatgaacgtggctgtgtttttaattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
ttttaat putative branch site (score: 3)
tgttttt CT-rich tract
tatttcattattttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgtctttgtcttcctattctatctaagagttattattttaattttatttcattattttgagctccatatgaacgtggctgtgtttttaattcagAAAATAAACAGCTTGGCCAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA