Sequence
atgc intronic sequence ATGC exonic sequencegtactttcctccatttgtgttactcgttttctttgctggatccatttgcagggatctgtttcttctgcactcgcttaccaatgtatgtgtgtatttttctagCATCTTGTGGCGCGCAAAGAGCAATCAGCACTTAGAGCAGTCTTAAAATGCATAGAAGAATACAAACTCGAGGAAGAATTCCCACCCGAGAATCTCAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14900.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G39330.1 (Glycine max), 3'ss of exon 2
gtactttcctccatttgtgttactcgttttctttgctggatccatttgcagggatctgtttcttc-tgcactcgcttaccaatgtat---gtgtgtatttttctagCATCTTGTGGCGCGCAAAGAGCAATCAGCACTTAGAGCAGTCTTAAAATGCATAGAAGAATACAAACTCGAGGAAGAATTCCCACCCGAGAATCTCAAGA
| ||| |||||||| ||||||| | | | ||| | | | || | | | || | | ||| | || ||||| || | || | || | |||||||| || ||||| || || || | |||||||| |||||||||||||| ||||| || |||||||| |||||||| ||||
-aaaagcgctctatttgtgtagt--attttcttgagttagtaga---agggggcttaatatattaacggatttttttttctttctatggtgaatgaattttggcagTACCTAGCTGCAAGGAAAGAGCAGTCTGCACTCAGGGCTGTGATTAAATGCATTGAAGAATACAAACTTGAGGATGAGTTCCCACCAGAGAATCTGAAGAMapped 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|164147000|gb|ES106054.1|ES106054EST: GATGATTCCAACAATTCTGGCCGATCTGCG CATCTTGTGGCGCGCAAAGAGCAATCAGCACTTAGAGCAGTCTTAAAATGC
genomic: GATGATTCCAACAATTCTGGCCGATCTGCGgtactttcct ... atttttctagCATCTTGTGGCGCGCAAAGAGCAATCAGCACTTAGAGCAGTCTTAAAATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagggatctgtttcttctgcactcgcttaccaatgtatgtgtgtatttttctagCATCTTGTGGCGCGCAAAGAGCAATCAGCACTTAGAGCAGTCTTAAAATGCATAGAAGAATACAAACTCGAGGAAGAATTCCCACCCGAGAATCTCAAGA
cgcttac putative branch site (score: 3)
tatttttct putative PPT
tatttttcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttcctccatttgtgttactcgttttctttgctggatccatttgcagggatctgtttcttctgcactcgcttaccaatgtatgtgtgtatttttctagCATCTTGTGGCGCGCAAAGAGCAATCAGCACTTAGAGCAGTCTTAAAATGCATAGAAGAATACAAACTCGAGGAAGAATTCCCACCCGAGAATCTCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA