Sequence
atgc intronic sequence ATGC exonic sequence...atttgggtcttgaatgacaatagtatatgctttgtaagcagcttttctgtaaatttgtagaggttttataataattatctgatctttgttaaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAATATATGGAAATACACTTTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51820.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 7
---------atttgggtcttgaatg-acaatagtatatgctttgtaagcagcttttctgtaaatttgtagaggttttataataattatctgatctttgttaaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAATATATGGAAATACACTTTCA
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ttcggcaaaaaccgaattgtcaacatgcgatagtataaacat-----gcaattttcctcaagtttattacatgatcaagtagcttaataagatgttc-----aattgcagTTCAACTATAGCAGTGGGCAGCCAGCACCAGAGACAATTACCGACCAAATATATGGAAACACACTTTCG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 7
---atttgggtcttgaatgacaatagtatatgctttgtaagcagcttttctgtaaatttgtaga---ggttttataataattatctgatctttgttaaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAATATATGGAAATACACTTTCA
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catacttttttctgtaac-atgtttgtggtcaatttttaag-actttatgtggaaatctgtcagtccgtgtttctaataa--atgtgtttgttgttgactc--cagTTTAATTACAGCAGTGGACAACCTGCACCAGAATCCATCACTGACAAGATTTATGGAAATACCCTGTCG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 7
--atttgggtcttgaatgacaatagtatatgctttgtaagcagcttttctgtaaatttgtagaggt---tttataataattatctgatctttgttaaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAATATATGGAAATACACTTTCA
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atactttttttttctaacatgtttgtggtcaatgtctaag-attttatgtgcaaatatgtcaatctgtgtttctaataaatgtct--ttgctgttgactc--cagTTTAATTACAGCAGCGGACAACCTGCACCAGAATCCATCACTGACAAGATTTATGGAAATACCCTGTCG
upper sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 7
------atttgggtcttgaatgacaatagtatatgctttgtaagcagcttttctgtaaatttgtagaggttttataataattatctgatctttgttaaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAATATATGGAAATACACTTTCA
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agatatattttg-catccaatgactggatcaaattatttgcaatt--ctctagttaaaattttctga---ctgaaaatgctgttgttttcatttttcatttcccagTTTAATTACAGCAGTGGACAACCTGCACCTGAAACCATCACAGACAAGATTTATGGGAACACTCTTTCGMapped 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|125044744|gb|EL117013.1|EL117013EST: TGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG TTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAA
genomic: TGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAGgtgaagtatc ... aaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAA
EST:
gi|124711266|gb|EH802668.1|EH802668EST: GAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG TTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAA
genomic: GAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAGgtgaagtatc ... aaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtaaatttgtagaggttttataataattatctgatctttgttaaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAATATATGGAAATACACTTTCA
atctgat putative branch site (score: 4)
ttttataataattatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgggtcttgaatgacaatagtatatgctttgtaagcagcttttctgtaaatttgtagaggttttataataattatctgatctttgttaaatttacagTTCAATTACAGCAGTGGTCAGCCTGCTCCTGAAACCATTACTGACAAAATATATGGAAATACACTTTCA
- - - - - - - -gacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatct