Sequence
atgc intronic sequence ATGC exonic sequence...atgtggaagtaatgtcaacaaatatgattttgtgatcaaatatgattttgtgaagagatcaaatatgattttgtgaagctatgtgtcttggtgttttcagGTCCGGAAGACAATGTGGCAGATTATTACCAGCAGCAAGTAGAGATGCTTGAGGGCTTTACTGAAATGGATGAACTTGCAGAACGTGGCTTTGTTCCTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39450.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G10580.1 (Glycine max), 3'ss of exon 1
--atgtggaagtaatgtcaacaaatatgattttgtgatcaaatatgattttgtgaagagatcaaatatgattttgtgaagctatgtgtcttg-gtgttttcagGTCCGGAAGACAATGTGGCAGATTATTACCAGCAGCAAGTAGAGATGCTTGAGGGCTTTACTGAAATGGATGAACTTGCAGAACGTGGCTTTGTTCCTGG
|||| | | | || | || | | | ||| ||||| || || | | |||| || | | ||| || | | |||||||| ||||| ||| | || || || || |||||||| ||||| ||||||||||||||||||||||||||| | ||||| ||||| ||| |||||||
ttgtgtgctttgagtat-ggcatctgtgctactaaagtgaaaggggatttcatg--gattttgtcttactttttttgttcttttctgttttatatttcttcagGTCAAGAAGATAATATTGCGGAGTACTATCAGCAGCAGGTAGAAGTGCTTGAGGGCTTTACTGAAATGGATGCTTTAGCAGAGCGTGGTTTTATTCCTGG
upper sequence: AT2G39450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G52280.1 (Glycine max), 3'ss of exon 1
atgtggaagtaatgtcaacaaatatgattttgtgatcaaatatgattttgtgaagag-atcaaatatgattttgtgaagctatgtgtcttggtgttttcagGTCCGGAAGACAATGTGGCAGATTATTACCAGCAGCAAGTAGAGATGCTTGAGGGCTTTACTGAAATGGATGAACTTGCAGAACGTGGCTTTGTTCCTGG
| || | | | || | | | | |||| ||||| || | || | | |||||| | | | | | |||||||| ||||| ||| | ||||| || || |||||||| || || ||||||||||||||||||||||||||| | ||||| ||||| ||| |||||||
gtatgctttgagtat-ggcatcctttctactaaattgaaatgggatttcatggatcttgtcttaattttttttgttctttttctgttatatatttcttcagGTCAAGAAGATAATATTGCAGAGTACTATCAGCAGCAGGTTGAAGTGCTTGAGGGCTTTACTGAAATGGATGCTTTAGCAGAGCGTGGTTTTATTCCTGG
upper sequence: AT2G39450.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g00020.t01 (Vitis vinifera), 3'ss of exon 1
-----atgtggaagtaatgtca-acaaatatgattttgtgatcaaatatgattttgtgaagagatcaaatatgattttgtgaagctatgtgtcttggtgttttcagGTCCGGAAGACAATGTGGCAGATTATTACCAGCAGCAAGTAGAGATGCTTGAGGGCTTTACTGAAATGGATGAACTTGCAGAACGTGGCTTTGTTCCTGG
| || | || | || | |||| | | || || | | | || |||||| ||| | || | | | | ||| | | ||||| ||||| ||||||| || ||||| |||||||| ||||| ||||| |||||||||| ||||||||||| | ||||| | ||| | | |
agagaaaatgaatctatagacacatgttgatgaatgggatatttaaaactagtgtgccaagagactaaacaatgttcatatcaattgttttgtttgacagCTCCTGGTCCAGAAGATGATGTGGCTGAGTATTATCAGCAGCAGGTAGAAATGCTGGAGGGCTTTAATGAAATGGATGCCTTGGCAGAGCATGGATATAT------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgtgaagagatcaaatatgattttgtgaagctatgtgtcttggtgttttcagGTCCGGAAGACAATGTGGCAGATTATTACCAGCAGCAAGTAGAGATGCTTGAGGGCTTTACTGAAATGGATGAACTTGCAGAACGTGGCTTTGTTCCTGG
tgttttc CT-rich tract
atcaaatatgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtggaagtaatgtcaacaaatatgattttgtgatcaaatatgattttgtgaagagatcaaatatgattttgtgaagctatgtgtcttggtgttttcagGTCCGGAAGACAATGTGGCAGATTATTACCAGCAGCAAGTAGAGATGCTTGAGGGCTTTACTGAAATGGATGAACTTGCAGAACGTGGCTTTGTTCCTGG
- - -gaagtaa
- - - - - - - -caacaaa
- - - - - - - - - - - - -gattttg
- - - - - - - - - - - - - - - - -gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -gaagaga