Sequence
atgc intronic sequence ATGC exonic sequencegttggtgtctttctcttcctattctatctaagagtttaatttttatttcattattttgagctccatatgaacctggcagtgttttaattcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
Basic information
species | Glycine max |
transcript | GLYMA10G43740.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 5
gttggtgtctttctcttcctattctatctaa--gagtttaatttttatttcattattttgagctccatatgaacctggcagtgtttta-attcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
|| | || | || | ||| | | ||| | | | | | ||| | | | | || |||| || || || ||||| | || || || | |||||||| |||||| | |||||||| || ||||| ||||| |||||||||||||||||
---------------------gtcagtgcaaatgcattcattttcttctgttttactgtatggttgcttctaacttctttatttggtgcatacagAGCATGAATCGCATGGCTCATTTGAAACGAGCCGAGTATGGGAAAGTTGATTTGGATTACGTGCTTGGAATTGGAGGCTTTGATTTGGAGAG
upper sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G180418_T03 (Zea mays), 3'ss of exon 10
gttggtgtctttctcttcctattctatctaagagtttaattt-ttatttcattattttgagctccatatgaacctggcagtgttttaattcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG--------
|| | | || | | | |||| ||||| | || | | || | ||| || | ||| | ||| || ||| | ||||||| || ||||| | |||||||| |||||| | ||||| ||||||||||| ||||| || |||||| |||||||
--------------------gttagtgttgcgtattcattctgctattgcattaccataagtttctaat-atcct--catttgcttagtacagGGTATCAACCACATGGCTAATTTGAAGCGAGCTGAGTATGGTAAAGTTGATTTGGACTATGTTCTTGGAATTGGAGGATTTGATCTGGAGAGGTTCCTTT
upper sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G180418_T01 (Zea mays), 3'ss of exon 10
gttggtgtctttctcttcctattctatctaagagtttaattt-ttatttcattattttgagctccatatgaacctggcagtgttttaattcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
|| | | || | | | |||| ||||| | || | | || | ||| || | ||| | ||| || ||| | ||||||| || ||||| | |||||||| |||||| | ||||| ||||||||||| ||||| || |||||| |||||||
--------------------gttagtgttgcgtattcattctgctattgcattaccataagtttctaat-atcct--catttgcttagtacagGGTATCAACCACATGGCTAATTTGAAGCGAGCTGAGTATGGTAAAGTTGATTTGGACTATGTTCTTGGAATTGGAGGATTTGATCTGGAGAG
upper sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 5
gttggtgtctttctcttcctattctatctaagagttt----aatttttatttcattattttgagctccatatgaacctggca-gtgttttaattcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
|| ||| ||| ||||| ||||| ||| | || | ||||| | | || || | | | | | | ||| || | |||| ||||||||| ||||| || | ||||||||| ||||||| || ||| ||||||||||||||||||| ||||| || |||||| | || ||
gtaggt-tctgcttcttctgattctttcttttttctctttgaacatctatttt-tctctgtgcactgcgttagcatttatgatgtggttatttccagACCATAAACAGCATGGCTCACATGAAGCGGACAAAGTATGGGAAGGTTGACTTGGATTATGTTCTTGGAATTGGAGGGTTTGATCTAGAAAG
upper sequence: GLYMA10G43740.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g08260.t01 (Vitis vinifera), 3'ss of exon 5
gttggtgtctttct-cttcctattctatctaagagtttaatttttatttcattattt-tgagctccatatgaacctggcagtgtt--ttaattcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
|||||| ||| || ||| || | || | ||| || || |||| || | || | | | ||| | | || | || ||||| ||||| |||||||| | | ||||||||||||| |||||||||| ||||||||||||| ||||| | || |||||||||||||||||
gttggtaccttgcttcttgcttggatggctttcatttttcttattgtttcgttttggatgtgttggactgtggtgtggtacttttgctgaaagcagAATATAAATCGCTTGGCTCATCTCAAGCGGACAGAGTTTGGAAAAGTTGACTTGGATTATGTACTTGGAGTAGGAGGCTTTGATTTGGAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttttatttcattattttgagctccatatgaacctggcagtgttttaattcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
ttttaat putative branch site (score: 3)
ttatttcattattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgtctttctcttcctattctatctaagagtttaatttttatttcattattttgagctccatatgaacctggcagtgttttaattcagAAAATAAACAGCTTGGCTAACTTAAAGCGGACAGAGTATGGAAAAGTTAACTTGGATTATGTTCTTGGCATTGGGGGCTTTGATTTGGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA