Sequence
atgc intronic sequence ATGC exonic sequencegtttgtctcattgtttttaagctagagaaacttgatgtttatctgattgctgtgtctagatccttaatgaggctatatcttaaccttacctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63490.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G37370.3 (Glycine max), 3'ss of exon 4
gtttgtctcattgtttttaagctagagaaacttgatgttt--atctgattgctgtgtctagatccttaatgaggctatatcttaaccttacctactg-cagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
| | || | || ||||||||| | ||| | | || || | ||| ||||| | | ||| | || | || |||| |||||||||||||| || || || || ||||| |||||| | |||||| |||| ||||||||||||||| ||||||| ||||| |||||||| |||||
-----gttggtagtgtata---tagagaaacacaacttttcaagttagttacttt-tctgtatcctgccttttga-atacatggctgatatatgttgacagGGAAATTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTTTGGCTTTACTAGACATAGCAAAGTGTTTGCATGATGCCATTGCCCGTATGGAAAGGGC
upper sequence: AT5G63490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G01470.1 (Glycine max), 3'ss of exon 2
gtttgtctcattgtttttaagctagagaaacttgatgtttatctgattgctgtgtctagatcctt-aatgaggctatatcttaaccttacctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
| | || | | | || || || | || ||| ||| |||| | | | ||| || | | | | ||| | | |||| | ||||||||||| || || || || ||||| |||||| |||| || | || ||||||||||||||||||||||| ||||| |||||||| |||
------gttggtattactcggagataggcacatgctaatt-tct-atttctgtatggtgccattggaataagtacaaagatca--tttatgtttt-cagGGAGGTTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTTGTTGCCATACTTGACATAGCAAAGTGTTTGTATGATGCCATTGCCCGTATGGAAAGGAA
upper sequence: AT5G63490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G38140.1 (Glycine max), 3'ss of exon 3
gtttgtctcattgtttttaagctagagaaacttgatgtttatctgattgctgtgtctagatccttaatgaggctatatcttaaccttacctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
||| | ||| | | ||| | || | | | | | | | ||| ||| | | | |||| | ||||||||||| || || || || ||||| ||||| |||| || | || ||||||||||||||||||||||| ||||| |||||||| |||||
---------gttggtattacacggagataggcacatgctaatt--actatttcggtacggtgccctttgaataaatacaaagatgattatgttttcagGGAGGTTCAGACATTTACCTGTGGTGGAGAATGGAGAAGTAGTTGCCATACTTGACATAGCAAAGTGTTTGTATGATGCCATTGCCCGTATGGAAAGGGC
upper sequence: AT5G63490.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv17s0000g01200.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtctcattgtttttaagctagagaaacttgatgtttatctgat-tgctgtgtctagatccttaatgaggctatatcttaaccttacctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
||| || || | || | | |||| | | ||| | |||| | |||| | | || | || | | || | | ||||||||| |||||||||||||| ||||| || ||||| || || ||||||||| |||| |||||||||||||| |||||||| |||||||| |||||||||||
-gttg-ctgataacctgaaaaccatgtttactt--tttccatccaacatgctat-tctacaac-ttgccaa--ctgaacactgtgctgattttttgcagGAAAGTTCAGACATTTGCCTGTTGTAGAGAATGGGGAGGTCATTGCTTTACTAGACATAGCAAAGTGTTTATATGATGCTATTGCTCGAATGGAGAGGGCMapped 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|19876521|gb|AU237352.1|AU237352EST: TGTTCTCTCAGAAACACTTGCTGTTGAAGCTCTNCAAAAGATGGTCCAAG GAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTAT
genomic: TGTTCTCTCAGAAACACTTGCTGTTGAAGCTCTCCAAAAGATGGTCCAAGgtttgtctca ... cctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattgctgtgtctagatccttaatgaggctatatcttaaccttacctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
ccttacct CT-rich tract
tatatcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtctcattgtttttaagctagagaaacttgatgtttatctgattgctgtgtctagatccttaatgaggctatatcttaaccttacctactgcagGAAAATTCAGACATTTGCCGGTTGTTGAAAATGGCGAAGTTATTGCTTTATTAGATATAGCAAAGTGTTTGTATGATGCAATTGCTCGTATGGAGAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG