Sequence
atgc intronic sequence ATGC exonic sequence...ttctctggttcttaggttaggttcttgtttgttccgttttaacaatttacctatcttattggagagcgatatttatgatgtgatatttgtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14210.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 4
---------------------------------ttctctggttcttaggttaggttcttgtttgttccgttttaacaatttacctatcttattggagagcgatatttatgatgtgatatttgtcttcctc---------------cagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT
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gttttactcttatgcttttatgttgcatttaattttttttgttattcattctttttttttttggttgcctttatcttaatagctcatattcactgttagtagcatttgtggattattgtttttttttttggggaaatgccttgaacagATAGCTGCTTGGAAGGATGAAGATGGAGATTGGTATGAAACTGGGCTTCATATCTTTT
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G410515_T02 (Zea mays), 3'ss of exon 4
ttctctggttcttaggttaggttcttgtttgttccgttttaacaatttacctatcttattggagagcgatatttatgatgtgatattt-gtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT------------------------------------------
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--gtctgataaatac-ttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 4
ttctctggttcttaggttaggttcttgtttgttccgttttaacaatttacctatcttattggagagcgatatttatgatgtgatattt-gtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT
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--gtctgataaatac-ttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv09s0002g00100.t01 (Vitis vinifera), 3'ss of exon 4
ttctctggttcttaggttaggttcttgtttgttccgttttaacaatttacctatcttattggagagcgat---attta-tgatgtgatatttgtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT
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----gcaatactaattgtataatagatttaacttcctacttaatttccccttttattgttggaagtttctttcatttagtgaaggctagtctctcttgatatagGTGGCTGCATGGAAAGATGAGGATGGAGACTGGTATGAGACAGGCCTACATATATTCT
upper sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1
ttctctggttcttaggttaggttcttgtttgttccgttt-taacaatttacctatcttattggagagcgatatttatgat----gtgatatttgtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT------------------------------------------
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--------------------gtgagtgtgcacccggcgagcgccaattcgtgcatcgtagcataaatggacaattgggctaaccgtgccaaccttttgctggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTACCCCAACATGATGAATGTCTTCAAGGAGCTAAMapped 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|116473796|gb|EG516388.1|EG516388EST: CAGGCCACAAACCTCTGTTGCTTGAAGCAAGAGATGTTCTTGGTGGAAAG ATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACAT
genomic: CAGGCCACAAACCTCTGTTGCTTGAAGCAAGAGATGTTCTTGGTGGAAAGgtactttgat ... cttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacctatcttattggagagcgatatttatgatgtgatatttgtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT
tatttgtcttcctcc CT-rich tract
atatttatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctctggttcttaggttaggttcttgtttgttccgttttaacaatttacctatcttattggagagcgatatttatgatgtgatatttgtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG