Sequence
atgc intronic sequence ATGC exonic sequencegtatatttttctcactctcgtggcattgttttcaacgggtctattcccggtataggccgacaaatcctgattcaatagagaataaagactaaaaaaataggaagtagagtaagaggaatgttgtcgctttcagGTGATGGTTTGTGGGATTCTTCTGGTAGTGATGGCAGTTGGGAACTTCATAAATACAGTAGAGACACTGATGGCAAAGTCAAGAGTTAAGGCAAAGATGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10430.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G44190.3 (Glycine max), 3'ss of exon 8
----------gtatatttttctcactct-cgtggcattgttttcaacgggtctattcccggtataggccgacaaatcctgattcaatagagaataaagactaaaaaaataggaagtagagtaagaggaatgttgtcgctttcagGTGATGGTTTGTGGGATTCTTCTGGTAGTGATGGCAGTTGGGAACTTCATAAATACAGTAGAGACACTGATGGCAAAGTCAAGAGTTAAGGCAAAGATGA
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gtactagtttgtttatccttgctactttacttcactttgtacaccaattgattgattggaacagaagaaaataaatccaGTAATATTTTGTTGCATAGATTAGCCT--TAGCCTTTATAATGATAGAAGCTCTTCGGG---CAGGTAATATTTTGCGGTGTTCTGTTGGTCTTAATGGCTGTTGGGAACTTTGCAAATACAGTACAGACTCTGATGGCAAAATCAAGATTTAAGGCAAAGATGA
upper sequence: AT4G10430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G38960.1 (Glycine max), 3'ss of exon 9
------gtatatttttctcactctcgtggcattgttttcaacgggtctattc-ccggtataggccgacaaatcctgattcaatagagaataaagactaaaaaaataggaagtagagtaagaggaatgttgtcgctttcagGTGATGGTTTGTGGGATTCTTCTGGTAGTGATGGCAGTTGGGAACTTCATAAATACAGTAGAGACACTGATGGCAAAGTCAAGAGTTAAGGCAAAGATGA
|| ||| || | | || | || |||| || || ||| | | | || | || || || | | | | | || ||| | | | ||||| || |||| || | || |||| | ||||| ||||||||||| |||||||||| |||| ||||||||||| |||||| |||||||||||||||
gtactagttcgtttgtccttgttacttgactttattttgtaca--tcaattgattgattggaacagaagcaaataaatccaGTAATATTTTGTTGCATAGATTAGCCATAGCCTTATAATTGATAGAACTCTTCGGGCAGGTAATATTTTGCGGTGTCCTGTTGGTCTTAATGGCTGTTGGGAACTTTGCAAATACAGTACAGACTCTGATGGCAAAATCAAGATTTAAGGCAAAGATGA
upper sequence: AT4G10430.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G38960.2 (Glycine max), 3'ss of exon 10
gtatatttttctcactctcgtggcattgttttcaacgggtct-attcccggtataggccgacaaatcctgattcaatagagaataaagactaaaaa----aataggaagtagagtaagaggaatgttgtcgctttcag-
||| | | || | || ||| | | | | | || || | |||| | | | | | | | |||||| || | | | | | || ||| ||| | | ||| | | || | | || | ||| | | || | | || | | ||| || | | || | || | | |
gtacagact-ctgatggcaaaatcaagatttaaggcaaagatgagaagaagcaagagcaagcagaggctgaattagcaagctgtcactttttttagttttgataggatcaggattttttgcactcatttcagttttgaccacagTGCAAGCTGGTGATAATTTTG-GCTTGTTGTAGCA-TCAATCATTTACAAGTTTAAGCATAAACATAAATT-TGGATTAAAATGATATTACGATACTACAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaataaagactaaaaaaataggaagtagagtaagaggaatgttgtcgctttcagGTGATGGTTTGTGGGATTCTTCTGGTAGTGATGGCAGTTGGGAACTTCATAAATACAGTAGAGACACTGATGGCAAAGTCAAGAGTTAAGGCAAAGATGA
gactaaa putative branch site (score: 2)
tcgctttc putative PPT
aaagactaaaaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatttttctcactctcgtggcattgttttcaacgggtctattcccggtataggccgacaaatcctgattcaatagagaataaagactaaaaaaataggaagtagagtaagaggaatgttgtcgctttcagGTGATGGTTTGTGGGATTCTTCTGGTAGTGATGGCAGTTGGGAACTTCATAAATACAGTAGAGACACTGATGGCAAAGTCAAGAGTTAAGGCAAAGATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG