Sequence
atgc intronic sequence ATGC exonic sequence...atgaagttgaatctgctagaatatatgcttattgcaggagaaggttgtgttctttactctaagcggatatatttgttttgaatgtgtgctgattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGACTCAGAATGTTAATGTAACTGTTTTACCATGCTTTGGATTGTCTGAAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G24180.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G24180.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os10g33420.1 (Oryza sativa), 3'ss of exon 10
------atgaagttgaatctg-ctagaatatatgcttattgcaggagaaggttgtgttctttactctaagcg-gatatatttgttttgaatgtgtgctgattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGACTCAGAATGTTAATGTAACTGTTTTACCATGCTTTGGATTGTCTGAAGAT
| | | || | | | | | | | | | | | ||| | | | | || || || | | | || ||| ||||| |||| || | |||||||| ||||| ||||| |||||||| | ||| ||||||||||| ||||| || || || || ||||| | |||| |||
tgcatcacaagcaagtgtcaaaccaaaccttctcccttgttccacatattcttgcatcatgtgttgcctgcacgagctaacagactagcatttgt--------tgcagAACAGCAAAGGATAATCCTCCGGTTACTTTTGCTATTGCTGCCTGTGAAACTCAGAATGTGAATGTGACAGTCTTGCCTGTATTTGGCCTCTCTGGAGAA
upper sequence: AT3G24180.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G33610.1 (Glycine max), 3'ss of exon 13
atgaagttgaatctgctagaatatatgcttattgcaggaga-aggttgtgttctttactctaagcggatatatttgttttgaatgtgtgctgattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGACTCAGAATGTTAATGTAACTGTTTTACCATGCTTTGGATTGTCTGAAGAT
|| | || | || | || | | || | | ||| | | | | | | | | | || | | | || ||||||||||| |||||||| ||||||||||| ||||| |||||||| | |||||| |||||||||||||| ||||||| ||| | ||||| ||||||||||
gtgtgggtgggtatgtatgtatttgtaattctcttgtctcctaaactgttatgtaaatgatgattttg-gtgtatatattaaggtcattccaatattgcagGACAGCGAAAGGAAACCCTCCTGTTACCTTTGCCATTGCTGCATGTGAGACACAGAATGTTAATGTTTCTGTTTTGCCAAGTTTTGGGCTGTCTGAAGAA
upper sequence: AT3G24180.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA20G33990.1 (Glycine max), 3'ss of exon 12
------atgaagttgaatctgctagaatatatgcttattgcaggagaaggttgtgttctttactctaagcggatatatttgttttgaatgtgtgctgattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGACTCAGAATGTTAATGTAACTGTTTTACCATGCTTTGGATTGTCTGAAGAT
|| || || | | | | | | || | | | ||| | | | | ||||||| | | | || ||||||||||| |||||||| ||||||||||| ||||| |||||||| | ||||| |||||||||||||| ||||||| ||| | ||||| ||||||||||
gtgtgggtgggaatgtatatatttgtaattctcctgtctcctaaactgctatgtaaatgatgattttggtctatatatt------aaggtcattccaatattgcagGACAGCAAAAGGAAACCCTCCTGTTACTTTTGCCATTGCTGCATGCGAGACACAGAATGTTAATGTTTCTGTTTTGCCAAGTTTTGGGTTGTCTGAAGGA
upper sequence: AT3G24180.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv05s0051g00910.t01 (Vitis vinifera), 3'ss of exon 10
atgaagttgaatctgctagaatatatgcttattgcaggagaaggttgtgttctttactctaagcggatatatttgttttgaatgtgtgctgattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGACTCAGAATGTTAATGTAACTGTTTTACCATGCTTTGGATTGTCTGAAGAT
| | | || | || | | | || || || || | ||||| | | | | | | | || ||| ||||| | |||| || ||||||||||| ||||| || ||||| | ||| ||||||||||||| ||| ||||| || |||| |||||| | |||||||
ttactgatcaaaaaaaaaaaaaaaaagttttctgtttgaattaattaactctgttactatggaatttcaagtcattctgaggattaagaaaatgttgtagGACTGCTAAAGAGAACCCTCCTGTTACTTTTGCTATAGCTGCATGTGAAACTCAGAATGTTAGTGTCACTGTGTTGCCATCATTTGGACTCTCTGAAGGAMapped 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|125069775|gb|EL135432.1|EL135432EST: GTCCTCTTACATCACAA GACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGAC
genomic: GTCCTCTTACATCACAAgcaagtcatc ... gattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgttctttactctaagcggatatatttgttttgaatgtgtgctgattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGACTCAGAATGTTAATGTAACTGTTTTACCATGCTTTGGATTGTCTGAAGAT
tgctgat putative branch site (score: 3)
atatatttgttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgaagttgaatctgctagaatatatgcttattgcaggagaaggttgtgttctttactctaagcggatatatttgttttgaatgtgtgctgattttgcagGACAGGCAAAGGAAATCCTCCTGTTACATTTGCGATTGCTGCTTCTGAGACTCAGAATGTTAATGTAACTGTTTTACCATGCTTTGGATTGTCTGAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA