Sequence
atgc intronic sequence ATGC exonic sequencegtttgcttcattcattgtctaggataatacagttattgtggaagttttaggtaaaatgttagtgacgttctttgtgcctttttttttttctcttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 5
gtttgcttcattcattgtctaggataatacagttattgtggaagttttaggtaaa-atgttagtgacgttctttgtgcctttttttttttctcttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
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----aaaaagtacaaacttacagggactaaaaacatatttaagcctacaaataattatgatagaaatgatgactta--ttttcttattggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCTGAGGAATACTTGAGGGCCTTGTTTGAGAGAATATCTAGAA
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G02610.1 (Glycine max), 3'ss of exon 4
gtttgcttcattcattgtctaggataatacagttattgtggaagttttaggtaaaatgttagtgacgttctttgtgcctttttttttttctcttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
| ||| || ||| | | || | | || || | | |||| || || | | | ||| ||||| | ||| || |||||||||||||||| || || |||||||||||||| || || || ||||||||||| || | ||| ||| |||| || ||| ||| || ||| | |
-----gtgtgctcacaatcct--atagttctgtaa--attgatgtacaaataattatgtcag--acatgatggcttattttctttttggttgttgagttatgcagATGTCTGCTGATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCAGAGGAATACTTGAGGTCCTTGTTTGAGAGAATATCTAGAA
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G45340.1 (Glycine max), 3'ss of exon 4
gtttgcttcattcattgtctaggataatacagttattgtggaagttttaggtaaaatgttagtgacgttctttgtgcctttttttttttctcttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
| | | | | ||| | | | |||| ||| | || | | | || | | | ||| ||||| ||||| || ||||||||||| |||| || || |||||||||||||| || || || ||||||||||| |||| ||| ||| |||| | ||| ||| || ||| | |
--ataaagtacaaacttacagggactaaaaacatattt---aagcctacaaataattatgatagaaatgatgacttattttctttttggttcttgagttatgcagATGTCTGCTAATGATTTCATAAGAAACAATCGTGGCATTGATGATGGAAAAGATTTGCCTGAGGAATACTTGAGGGCCTTGTTTGAGAGAATATCTAGAA
upper sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 4
gtttgcttcattcattgtctaggataatacagttattgtggaagttttaggtaaaatgttagtgacgttctttgtgcctttttttttttctc-----ttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
| | | | | || | | |||||| || |||| | | | | || ||| |||| | | || |||||| | || || || ||||||| ||||||| ||||| |||||||||||||| ||||| ||||||||||||||||||| |||||| |||||||| |||||||| ||||| |||
----gtatactcaaaaatttaatttga---agttatga--gatgtttaatatcataacttgctgaatttctgtttattattaatttttttttggtcattaaaatatgcagATGTCGCCTGATGATTTTATAAGAAACAATCGTGGCATAGATGACGGAAAAGATTTACCTGAGGACTATATGAGATCATTGTATGAACGGATATCAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaaaatgttagtgacgttctttgtgcctttttttttttctcttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
ttctttgtgccttttt CT-rich tract
tttttttttttctctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgcttcattcattgtctaggataatacagttattgtggaagttttaggtaaaatgttagtgacgttctttgtgcctttttttttttctcttggaacatatagATGTCTGCTGATGACTTTATCAGAAACAATCGTGGAATAGACGACGGAAAAGATTTACCTGCGGACTACATGAGATCGCTGTATGAAAGGATAACAAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC