Sequence
atgc intronic sequence ATGC exonic sequencegcaagtatacaaaccctttttatcactcttgactgatataaatgagagatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18180.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G05980.1 (Glycine max), 3'ss of exon 5
gcaagtatacaaac-cctttttatcactcttgactgatataaatgagagatattcttactacttagctaatttgatatt----cagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
| || | | | || || |||| | | ||| | | | | || | || || | | | ||| | |||||||||||||||||||| |||||||| ||||||||||||||||||| ||
gtgagaacaaagacattttcttataatatctacctgtttttgtcaataaattaagattttatctaattgagcttataatttaacagGTTCTTGGCAACAAGTATCAAAGCAAATTGCTTGAAATAATTGATGAGAG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G24670.1 (Glycine max), 3'ss of exon 5
gcaagtatacaaaccctttttatcactcttgactgatataaatgagagatattcttactacttagctaatttgatatt----cagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
| || | | | ||| | | | | | | | ||| | | || || | | | ||| | |||||||||||||||||||| |||||||| |||||||| |||||||||| ||
gtgagaacaaagaccttatcctaaatatctacatctttttgtcaagaaaataggattttatctaattgagcttataattcatcagGTTCTTGGCAACAAGTATCAAAGCAAATTGCTTGAGATAATTGATGAGAG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G07660.1 (Glycine max), 3'ss of exon 5
gcaagtatacaaaccctttttatcactcttgactgatataaatgagagatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
| |||| | ||||| | | | | || |||| || | ||| |||| | | | || |||||||||||||||||||||| | | ||| ||||| |||||||||||||| ||
gtgagtacataaaccttatcc--taattctgcttgattggtcagaaaagtataattacgtcactcgaacataaattttcagGTTCTTGGCAACAAGTATGACACCAAATTGCTAGAAATAATTGATGCAAG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G01270.1 (Glycine max), 3'ss of exon 6
gcaagtatacaaaccctttttatcactcttgactgatataaat---------gagagatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
| || || | || | |||| | | || || | || || | || | | | | |||| | ||||| || || ||||| ||||| ||||||||||||||||| |||||||| ||
gtaaacatttttagtctgctgatcaatttgaaccaatgttgattttcatttaagcagggacactgaacatgttaatgatttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG
upper sequence: AT2G18180.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G12270.1 (Glycine max), 3'ss of exon 5
gcaagtata---caaaccctttttatcac----tcttgactgatataaatgag-agatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
| ||| || | | ||||| | || || | | | | || || |||| || | || ||| | ||||| || || ||||| ||||| ||||||||||||||||| |||||||| ||
gtaagcattttttatatacttttcaccatgaagcaatgtacgtttcagttaagtaggagcacttaatagattactgctttattgaccagGTCCTAGGTAACAAATACCAGAGCAAGTTGCTTGAAATCATTGATGCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgactgatataaatgagagatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
taatttgatattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtatacaaaccctttttatcactcttgactgatataaatgagagatattcttactacttagctaatttgatattcagGTTCTTGGCAACAAGTACCAAAGCAAGTTGCTTGAAATAATTGATGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG