Sequence
atgc intronic sequence ATGC exonic sequencegtatatgtgtataaaaatttgaactttgttaggtgctttatatgtaatgttgttgatttgtgtagtctttgtttgtaatttgtagTGTGGAGATTTACAAACACAATAAGGAAGAAAGGATAGCTAGAACTTGGGGAACTACTTCTCCAGGATTGCCTTATGTGGAAGAATATATTACTCCATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19920.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G06940.1 (Glycine max), 3'ss of exon 1
--gtatat-gtgtataaaaat-ttgaactttgttaggtgcttta-tatgtaatgttgttgat-ttgtgtagtctttgtttgtaatt---------tgtagTGTGGAGATTTACAAACACAATAAGGAAGAAAGGATAGCTAGAACTTGGGGAACTACTTCTCCAGGATTGCCTTATGTGGAAGAATATATTACTCCATCT
||| | | |||||| | ||||| | | | | | | || | | ||| | | || || || || ||| || ||| | || || ||||| || || ||||||||||| |||||||||||||||||||| ||| |||| |||||||| ||||| || || |||||||| |
tgttattttgaaaataaaagtattgaagtgaactggctatctaagtaaatttctgtcttggtgtctcgtggttttcattaaccattaagctcctatgcagTATTGAAATCTACAAGCATAACAAGGAAGAAAGAATAGCTAGAACTTGGGGAACAACTGCTCCTGGATTGCCATATGTTGAGGAGGTGATTACTCCGGCA
upper sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G05020.1 (Glycine max), 3'ss of exon 2
gtatatgtgtataaaaatttgaactttgttaggtgctttatatgtaatgt-tgttgatttgtgtagtctttgtttgtaatttgtagTGTGGAGATTTACAAACACAATAAGGAAGAAAGGATAGCTAGAACTTGGGGAACTACTTCTCCAGGATTGCCTTATGTGGAAGAATATATTACTCCATCT-------------------------------------------------
||| | | | ||| | ||| || | | | | | | ||| | || || ||||| || || ||||||||||| ||||||||||||| |||||| ||| |||| |||||||| ||||| || || |||||||| |
----------------------------------tttttgtct-tggtgtctcttggctttcattaaccattaagctcctacgcagtattgaaatctacaagcataacaaggaagaaagaatagctagaacttagGGAACAACTGCTCCTGGATTGCCATATGTTGAGGAGGTGATTACTCCGGCAGGAAATTGGCTTATTGGAGGAGATTTGGAAGTGCTAAAACCTATCAAATMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|116416085|gb|EG458677.1|EG458677EST: AATGTTGCTCTTGTTTGCCCTCAAGGAGATATCATTGGTTCTCTCCGAAG TGTGGAGATTTACAAACACAATAAGGAAGAAAGGATAGCTAGAACTTGGGG
genomic: AATGTTGCTCTTGTTTGCCCTCAAGGAGATATCATTGGTTCTCTCCGAAGgtatatgtgt ... taatttgtagTGTGGAGATTTACAAACACAATAAGGAAGAAAGGATAGCTAGAACTTGGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aggtgctttatatgtaatgttgttgatttgtgtagtctttgtttgtaatttgtagTGTGGAGATTTACAAACACAATAAGGAAGAAAGGATAGCTAGAACTTGGGGAACTACTTCTCCAGGATTGCCTTATGTGGAAGAATATATTACTCCATCT
tgttgat putative branch site (score: 4)
tttatatgtaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgtgtataaaaatttgaactttgttaggtgctttatatgtaatgttgttgatttgtgtagtctttgtttgtaatttgtagTGTGGAGATTTACAAACACAATAAGGAAGAAAGGATAGCTAGAACTTGGGGAACTACTTCTCCAGGATTGCCTTATGTGGAAGAATATATTACTCCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA