Sequence
atgc intronic sequence ATGC exonic sequencegtagtcttttctctctatggtatgatctttcctacagtttttgagtgccaatatgcttcttcttttttagtgcaatcctgagttgtttttcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G10050.1 (Glycine max), 3'ss of exon 1
gtagtcttttctctctatggtatgatctttcctacagtttttgagtgccaatatgcttcttcttttttagtgcaatcctg-agttgtttttcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
|||| | || |||| | |||| || | | || | |||||| || || | || || | | || ||| ||||| |||||||| ||||| ||||| ||||| ||| ||||||||||||| || ||||| ||||||||||||||||| |||||||||
--------------gtatgtaa--atgtttcgtgagtattttaagatct--tctgttgtctcttttctaaggctctgaaacagatgctgcttcttgacagGGAAACCGGAGCATTATGTGCAATGAAGGAAGTAGAGTTATTTCCTGATGATCCAAAATCTGCAGAGTGTATAAAGCAGTTAGAGCAG
upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G20460.1 (Glycine max), 3'ss of exon 3
gtagtcttttctctctatggtatgatctttcctacagtttttgagtgccaatatgcttcttcttttttagtgcaatcctg-agttgtttttcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
| ||| || |||| | |||| || | | || | | |||| || || | || |||| | || ||| ||||| |||||||| ||||| ||||| ||||| || ||||||||||||| || ||||| || |||||||||||||| |||||||||
---------------gttcgta-aatgtttcatgagtattttaagatct--tctgttgtcttttttctaaggctctgaaacagatgttgcttcttgacagGGAAACCGGAGCATTATGTGCAATGAAGGAAGTAGAATTATTTCCTGATGATCCAAAATCTGCTGAGTGTATAAAGCAGTTAGAGCAG
upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G06200.1 (Glycine max), 3'ss of exon 5
gtagtcttttctctctatggtatgatctttcctacagtttttga-gtgccaatatgcttcttctt----ttttagtgcaatcctgagttgtttttcat--ttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
||| || | | |||| ||| | || | || || | | || || ||||| || || || | || | ||||| | | ||| ||||||||||||||||||| ||||| |||| || ||||| ||||||| || || || |||||||| |||||||| |||||||||
gtatgctatgttatcta--gtacaagtttcataagcattaatgctatttccattctctctttcttggaattgaagctcatttaggactccttttttttcctcacagAAAAACTGGAGCATTGTGTGCAATGAAGGAAGCGGAAATATTTTCTGATGATCCAAAGTCTGCAGAGTGCATAAAGCAGTTAGAGCAG
upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G39070.1 (Glycine max), 3'ss of exon 4
gtagtcttttctctctatggtatgatctttccta--cagt-ttttgagtgccaatatgcttcttcttttttagtgcaatcctgag----ttgtttttcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
||| | | |||| | || |||| || || | |||| || | || || | | || | || | ||||| ||| | || ||||||||||||||||||| ||||| |||| || ||||| ||||||| || || || |||||||| |||||||| |||||||||
gtatatctgtggttctagtgctacatttttcataagcattattttaagctcttccattctctctttcttcgaagctcgtctaaaacatattgttgttc-ctcatagAAAAACTGGAGCATTGTGTGCAATGAAGGAAGCAGAAATATTTTCTGATGATCCAAAGTCTGCAGAGTGCATAAAGCAGTTAGAGCAG
upper sequence: AT5G66850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s1194g00010.t01 (Vitis vinifera), 3'ss of exon 1
gtagtcttttctctctatggtatgatctttcctacagtttttgagtgccaatatgcttc--ttcttttttagtgcaatcctgagtt----gtttttcatttg-cagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
| | | | || || || ||| | | | | || || || ||| | || |||||| | ||| ||||||| | | ||| ||||||||||| | ||||| |||||||||||||| | ||||||||||||| ||||| |||||| |||||||||| |||||||||
------gtatgtgaatttgacatattcattctgttaatgtctctgttacagtaaactttaatatttatttagtatttgtttttgttttttgtttttcctctaacagAGAAACTGGAGCTCTATGTGCAATGAAAGAAGTTGAATTGCTTCCTGATGACCCAAAATCTGCAGAGAGTATAAAGCAGTTAGAGCAGMapped 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|47831783|gb|CK121467.1|CK121467EST: AAGCTAATAGGTCGTGGTACTTTTGGAAGTGTTTACGTTGCAAGCAACAG CGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGA
genomic: AAGCTAATAGGTCGTGGTACTTTTGGAAGTGTTTACGTTGCAAGCAACAGgtagtctttt ... tcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGA
EST:
gi|86058391|gb|DR354148.1|DR354148EST: AAGCTAATAGGTCGTGGTACTTTTGGAAGTGTTTACGTTGCAAGCAACAG CGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGA
genomic: AAGCTAATAGGTCGTGGTACTTTTGGAAGTGTTTACGTTGCAAGCAACAGgtagtctttt ... tcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgccaatatgcttcttcttttttagtgcaatcctgagttgtttttcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
tttttcattt CT-rich tract
ttctttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtcttttctctctatggtatgatctttcctacagtttttgagtgccaatatgcttcttcttttttagtgcaatcctgagttgtttttcatttgcagCGAAACTGGAGCATTGTGTGCGATGAAAGAAGTTGAGCTATTTCCTGATGACCCCAAATCCGCAGAGTGTATAAAGCAATTAGAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG