Sequence
atgc intronic sequence ATGC exonic sequencegtaaagtccaaaactttgtaccctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G42960.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 5
gtaaagtccaaaactttgtaccctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
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-----gtattattcttttttctaacccatacctgctcatttgctttgtgtctttaca-atga----cttatagagtt-taactttcctcatccatttttcttgcttcagATATGTTGCACCTGAATATGCTAATACTGGAATGTTAAATGAAAAGAGTGACGTTTACAGTTTTGGCGTTCTCTTGTTAGAAACTGTGACAGGAAGGAAT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G42170.2 (Glycine max), 3'ss of exon 4
gtaaagtccaaaactttgtaccctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
| || || || | || | || || || ||||| | | ||| | ||| | || | | | |||||| |||| |||||| ||||| ||||| |||||||||||||||||| | ||||| || | |||||| || || ||||||||||| | || |||||||| | ||||| | |||
---gtatgcagaatgtttcagtatct----actatatagatt-ttatt-------taaaggattgcattaatagaaacttactcatgttggacctgttcccaatttcagTTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTTGAAGCAGTTACTGGAAGGGAT
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 4
gtaaagtccaaaactttgtaccctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT-
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--tatgcacatgtttcagtatctacttgactactttatagattttatt-------taaaggattgcataaatagaaacttattcctattggacctgttcccaatttcagtTATGTGGCACCGGAATATGCTAATACAGGTTTGTTAAATGAGAGGAGTGACATTTACAGCTTTGGTGTTCTCCTGCTAGAAGCAGTTACTGGAAAGGATC
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 4
gtaaagtccaaaactttgtaccctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
||| | | ||| ||| | ||| | | ||||| | | || | | ||| | || || || | ||||||| | | |||||| ||||| ||||||||||||||||| | ||| | ||||| || |||||||| || || |||||||||||| | | || ||||| | ||||| | ||
gtata--cagaaaatttattatctctt-------------tccttattttatacttaaaggatttgtacacttaggaac--------tcacttttgttttggatttcagTTATGTGGCACCAGAATATGCTAACAGCGGTTTGTTAAATGAGAAGAGTGACATTTACAGCTTTGGTGTCCTCTTGCTGGAAGCAGTTACTGGAAGGGAC
upper sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 6
gtaaagtccaaaactttgt----accctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattga-tgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
||| || | | || | | | ||| | | ||| ||| || | | | || | | ||| | ||| || | ||| | | | |||||| ||||| |||||||||||||||||||| || | ||||| || ||||||||||| || ||||||||||| | || || ||||| | ||||| | |||
gtat-gtttatatgttcatcttaagtcccctttagtctttatagtttttccacctgtatgatataaattttttatgagagcctcagaacctgacatcttttctctggatttcagTTATGTGGCACCAGAATATGCTAATACTGGCTTGTTAAATGAGAAGAGTGATATCTACAGCTTTGGTGTTCTCCTGCTGGAAGCAGTTACTGGAAGGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
ttgttttc CT-rich tract
tttttgttattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagtccaaaactttgtaccctcctcaggccattaaggttattattatcttctcagatgatgtccttacaaagaaatcattgatgttgtttttgttattgttttcagATATGTAGCACCAGAATATGCTAATACAGGTCTTTTAAACGAAAAGAGTGATATATATAGCTTTGGTGTCTTGCTTCTTGAAGCTATAACTGGTCGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC