Sequence
atgc intronic sequence ATGC exonic sequence...ttttttttctcgcctacgtttaaatctagtattctagagcaagtgtttcttttgcgattcttacgcatataaatgtcaaaactctctgtgttttccgcagATGCGGGCATGAGTTTTGCTACTCGTGTGGAGCAGAGTACAGAGAAGGGCAACAGACTTGCACGTGTGCTTTTTGGGACGATGATGAAGAAGAACAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G19670.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G19670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G13240.1 (Glycine max), 3'ss of exon 2
ttttttttctcgcctacgtttaaatc-tagtattctagagcaagtgtttcttttgcgattcttacgcatataaatgtcaaaactctctgtgttttccgcagATGCGGGCATGAGTTTTGCTACTCGTGTGGAGCAGAGTACAGAGAAGGGCAACAGACTTGCACGTGTGCTTTTTGGGACGATGATGAAGAAGAACAAGAA
||| | | || | | | | | ||| | ||| || | | ||| || | || || ||| || || ||||||||||||| || ||||| || || ||| |||||||||||||||| ||| |||||| | |||||| || ||| | ||| | |
aaaaaagcctcactaggaaggacatgatgacaagtttatgtataggttg-tgttgtagtttaagcttttctaatagttttctattctcgtcttaatttcagGTGTGGTTATGAGTTTTGCTATTCATGTGGTGCGGAATACCGAGAAGGGCAACAGACATGCCAGTGTGCATATTGGGATGAAGATAACTCTGAAGACTCA
upper sequence: AT4G19670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0042g01130.t01 (Vitis vinifera), 3'ss of exon 2
ttttttttctcgcctacgtttaaatctagtattctagagcaagtgtttcttttgcgattcttacgcatataaatgtcaaaactctc---tgtgttttccgcagATGCGGGCATGAGTTTTGCTACTCGTGTGGAGCAGAGTACAGAGAAGGGCAACAGACTTGCACGTGTGCTTTTTGGGACGATGATGAAGAAGAACAAGAA
||| ||| || | | | || | || |||| ||| || || || | | || | || | || | |||| || ||||||||||| ||||| || ||||| || ||||||||||| || |||||||| || ||||| ||||||||||| || | ||| |
-tttatttttcatttgcact-ggataaaccgaatgagctcaag-gttgacatttcggtttatttagacatgatcacacttgcttacatgcgtaacaactgcagGTGTGGGCATGAGTTCTGCTATTCTTGTGGTGCGGAGTACAGAGACGGACAACAGACCTGTCAATGTGCATTTTGGGACGAAGAGAACTCTGAAGACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttttgcgattcttacgcatataaatgtcaaaactctctgtgttttccgcagATGCGGGCATGAGTTTTGCTACTCGTGTGGAGCAGAGTACAGAGAAGGGCAACAGACTTGCACGTGTGCTTTTTGGGACGATGATGAAGAAGAACAAGAA
ttcttac putative branch site (score: 2)
ctctctgtgttttcc putative PPT
atataaatgtcaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttttttctcgcctacgtttaaatctagtattctagagcaagtgtttcttttgcgattcttacgcatataaatgtcaaaactctctgtgttttccgcagATGCGGGCATGAGTTTTGCTACTCGTGTGGAGCAGAGTACAGAGAAGGGCAACAGACTTGCACGTGTGCTTTTTGGGACGATGATGAAGAAGAACAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC