Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctgctctttcgtttcatttgatgtctagtctctcatattatatttctatgttgttgttgtaaacacaagttttttacatttccagGTTGTTGATGATTGGCCAGGATTGCCTCGAGGTGTGAAATTTGATCCATCTGATCCTGAGATCATATGGCATTTGCTAGCCAAATCTGGTTTGTCAGGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25580.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G11140.1 (Glycine max), 3'ss of exon 2
----gtatgtctgctctttcgtttcat--ttgatgtctagt-----ctctcatattatatttctatgttgttgttgtaaacacaagttttttacatttccagGTTGTTGATGATTGGCCAGGATTGCCTCGAGGTGTGAAATTTGATCCATCTGATCCTGAGATCATATGGCATTTGCTAGCCAAATCTGGTTTGTCAGGGT
|||| | | ||| | | || | | || |||| | || || | || | | | | |||||| | |||| | | || ||||| || ||||| |||||| ||||||||||||||||||| |||||||| ||||| ||||| || ||| ||| | || |
agagttatggttaaaaataaaaaacataatgaaggtatgattaaaactttcatcctttaaatcc-taaagtc-tagcatttgaactttttttctgatgatagGTAGCACAAGAGTGGCCTGGCTTGCCAAAAGGTGTCAAATTTGATCCATCTGATCAGGAGATCATTTGGCACTTGCTTGCAAAAGTTGGGGTAGGAGATT
upper sequence: AT1G25580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G34730.1 (Glycine max), 3'ss of exon 1
-------------gtatgtctgctctttcgtttcatttgatgtctagtctctcatattatatttctatgttgttgttgtaaacacaagttttttacatttccagGTTGTTGATGATTGGCCAGGATTGCCTCGAGGTGTGAAATTTGATCCATCTGATCCTGAGATCATATGGCATTTGCTAGCCAAATCTGGTTTGTCAGGGT
|| || ||| || |||| ||| | ||| | ||| || || |||||| | || | | ||| | || |||| | | || ||||| ||| | ||| |||||| ||||||||||||||||||| ||||| |||||||| ||||| || ||| |||| | |
tttgcttatacatataagttcaagacttcattct-tttgtcccaaagtattgcat-tcatagttgta-gttgttctcttacatttgaaacttt-atgttgttagGTAGCCCAAGAATGGCCTGGACTACCTTTAGGTGTTAAATTTGATCCATCTGATCAAGAGATAATATGGCACTTGCTTGCAAAAGTTGGTGCTGGAAATT
upper sequence: AT1G25580.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0011g02990.t01 (Vitis vinifera), 3'ss of exon 2
-gtatgtctgctctttcgtttcat-ttgatgtctagtctctcatattatatttcta-----tgttgttgttgtaaacac--aagttttttacatttccagGTTGTTGATGATTGGCCAGGATTGCCTCGAGGTGTGAAATTTGATCCATCTGATCCTGAGATCATATGGCATTTGCTAGCCAAATCTGGTTTGTCAGGGT-
| ||| | || | || || | | | ||| | | | | |||| |||| | || || | | | ||| |||||| | | || ||||||||||| ||| ||||||||||||||||||||||||||| ||||||||||||||||| || || ||| ||| | | | |
tgattgtacagttattgaagttatatttttatattatcttgcctgatcttcttctggcagctgttaatatttagaatgtttggaaactgtccttttgcagGTTACTCAGGAGTGGCCAGGATTACCTAGAGGTGTGAAATTTGATCCATCTGATCAGGAGATCATATGGCATTTACTTGCAAAAGTTGGAGT-TGGGAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcatattatatttctatgttgttgttgtaaacacaagttttttacatttccagGTTGTTGATGATTGGCCAGGATTGCCTCGAGGTGTGAAATTTGATCCATCTGATCCTGAGATCATATGGCATTTGCTAGCCAAATCTGGTTTGTCAGGGT
ttttttacatttcc CT-rich tract
tattatatttctatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctgctctttcgtttcatttgatgtctagtctctcatattatatttctatgttgttgttgtaaacacaagttttttacatttccagGTTGTTGATGATTGGCCAGGATTGCCTCGAGGTGTGAAATTTGATCCATCTGATCCTGAGATCATATGGCATTTGCTAGCCAAATCTGGTTTGTCAGGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA