Sequence
atgc intronic sequence ATGC exonic sequencegttcaatgcttaaatttacttaattgttaaaatgctcaaattatattttgtgatttgtttattaatttttaacttcttaaataaataactggctctattttttatatcctcgacttcttcattccttcactcccgtcacttattactagttttgtcttgcttttgaaacagATATATGGTGCTAGCGTCAATGGTCCAGTTCGGCACAAATGTCTTTCTGTCATTGGAAAATTGATGTATTTCAGCACAGCTGAGATGATCCAGTCTTTAC
Basic information
species | Glycine max |
transcript | GLYMA04G00530.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G049141_T02 (Zea mays), 3'ss of exon 6
gttcaatgcttaaatttacttaattgttaaaatgctcaaattatattttgtgatttgtttattaatttttaacttcttaaataaataactggctctattttttatatcctcgacttcttcattccttcactcccgtcacttattactagttttgtcttgcttttgaaacagATATATGGTGCTAGCGTCAATGGTCCAGTTCGGCACAAATGTCTTTCTGTCATTGGAAAATTGATGTATTTCAGCACAGCTGAGATGATCCAGTCTTTAC
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---------------------------------------gtca-gtcttgtcttattaatgttctctttgatgttgttaatggtaatgctgatgtggtattacgggacattgttgctatcatgttggtgt----gatactta-----aggacttcaatacctt--gaacagGTGTATGGCTCTAGTGTAAGTGGACCAATACGGCACAGGTGCTTATCTGTCATTGGGAAATTAATGTACTATAGCTCAGCTGAGATGATCCAGTCTCTCC
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 6
gttcaatgcttaaatttacttaattgttaaaatgctcaaattatattttgtgatttgtttattaatttttaacttcttaaataaataactggctctattttttatatcctcgacttcttcattccttcactcccgtcacttattactagttttgtcttgcttttgaaacagATATATGGTGCTAGCGTCAATGGTCCAGTTCGGCACAAATGTCTTTCTGTCATTGGAAAATTGATGTATTTCAGCACAGCTGAGATGATCCAGTCTTTAC
||| | ||| | || | | || | || | || | || | | | || | |||| || |||||| ||||||| |||||| |||| ||||||||| | |||| || |||||||| || ||||||||||| |||||||||||||||| | || ||||| || ||| ||
------------------------------------------------------------------------------------gtaattt-ttctctgcgttggctacaagataatgctcatactac-ctgctgttttgtctaattattcttgtttt-cttttgcaacagATCTATGGTTCTAGTGTCAATGGTACGATTCGCCATAAATGTCTCTCAGTCATTGGAAAGTTGATGTATTTCAGCAGTTCAGAAATGATTCAATCTCTAA
upper sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 6
gttcaatgcttaaatttacttaattgttaaaatgctcaaattatattttgtgatttgtttattaatttttaacttcttaaataaataactggctctattttttatatcctcgacttcttcattccttcactcccgtcacttattactagttttgtcttgcttttgaaacagATATATGGTGCTAGCGTCAATGGTCCAGTTCGGCACAAATGTCTTTCTGTCATTGGAAAATTGATGTATTTCAGCACAGCTGAGATGATCCAGTCTTTAC
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---------------------------------------------------------------------------------------gtaagttttctagttcacttggttagcagcatacagttcatagtttctttagttattggta-ttttttcttgtc----aaccagATCTATGGATCCAGTGTGAATGGCCCTGTTCGCCATAAATGTTTGTCAGTTATTGGAAAATTAATGTACTTCAGCACCGCAGATATGATCCAGTCTTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcattccttcactcccgtcacttattactagttttgtcttgcttttgaaacagATATATGGTGCTAGCGTCAATGGTCCAGTTCGGCACAAATGTCTTTCTGTCATTGGAAAATTGATGTATTTCAGCACAGCTGAGATGATCCAGTCTTTAC
ttttgtcttgctttt CT-rich tract
ttattactagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcaatgcttaaatttacttaattgttaaaatgctcaaattatattttgtgatttgtttattaatttttaacttcttaaataaataactggctctattttttatatcctcgacttcttcattccttcactcccgtcacttattactagttttgtcttgcttttgaaacagATATATGGTGCTAGCGTCAATGGTCCAGTTCGGCACAAATGTCTTTCTGTCATTGGAAAATTGATGTATTTCAGCACAGCTGAGATGATCCAGTCTTTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG