Sequence
atgc intronic sequence ATGC exonic sequencegtatttcactttcctggttcactttgttagagttttccctggatcgttcaattcaatgaagattttgctttttttgacaaatttagGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G35730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G35730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g37510.1 (Oryza sativa), 3'ss of exon 2
-----------gtat-ttcactttcctggttcactttgttagagttttccctggatcgttcaattcaatgaagattttgctttttttgacaaattt--agGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGC
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tgcagattggaatatgtgcatggtatttcttgagtgaaaaaacaacatgcttatgatgctgatcatatttctcatgaagctatttttgggctttttacagGTTGAGCATGTCATTAGAGAACAGAACATTATGGCAGCGAATGAGATCATTGATCTTTTCTGTGAGCTGATTGTTACACGCCTTCCCATCATTGCAAAGC
upper sequence: AT4G35730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G012413_T01 (Zea mays), 3'ss of exon 2
---------gtatttcactttcctggttcactttgttagagttttccctggatcgttcaattcaatgaagatttt--gctttt---tttgacaaattt--agGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGC
||| || || ||| | |||| | | |||||| | || | | | |||| ||||| | ||||||| ||||| || |||||||||||| || |||||| ||||| ||||||||||| ||||| || || |||||| | || || |||||||| | || |
tttcttatgatatcctgtgcaccatattttcttc--tggagtatgttagaaacaaaacaattctgcagttttctttaacatatggatttggcaaatctgcagGTTGAACATGTAATTAGGGAACAGAACTTTATGGCAGCCAACGAGATCATTGAGCTCTTCTGCGAGCTGATTGTTACACGCCTTCCTATCATCGCAAAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttccctggatcgttcaattcaatgaagattttgctttttttgacaaatttagGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGC
ttttgac putative branch site (score: 3)
tttttttgacaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcactttcctggttcactttgttagagttttccctggatcgttcaattcaatgaagattttgctttttttgacaaatttagGTTGAGCATGTGATAAGGGAACAGAACATTCAGGCAGCAAACGAAATCATTGAGCTTTTCTGTGAACTTATTGTTTCTCGTCTCACTATCATCACTAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT