Sequence
atgc intronic sequence ATGC exonic sequence...aaatttcctaaaataacaagctatttcatgactgaaatagttacttcggcaaacgttagtccctgatcatacttattcccattcttttggtattttccagAATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGAGGTGTTCTTGTGTTGTGTGCAAATACAATCCATTATCATAGTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G51660.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g18010.2 (Oryza sativa), 3'ss of exon 4
--aaatttcctaaaataacaagctatttcatgactgaaatagttacttcggcaaacgttagtccctgatcatacttat--tcccattcttttggtattttccagAATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGAGGTGTTCTTGTGTTGTGTGCAAATACAATCCATTATCATAGTCAG
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ttccattgcgtttaagcactggatttatt-tgactctatatataacttc--ttgccattacaaaataat-atacttaccattacaaagtgtttgttcctttcagAATCTGCCCCACGATGCATACCAACTTCTTGCAGTGCCTCCCCCTATTAGTGGTGTTCTTGTGATCTGTGCAAATTCCATCCATTACCATAGTCAG
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G455115_T01 (Zea mays), 3'ss of exon 5
aaatttcctaaaataacaagct-atttcatgactgaaatagttacttcggcaaacgttagtccctgatcatacttattcccatt-cttttggtattttccagAATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGAGGTGTTCTTGTGTTGTGTGCAAATACAATCCATTATCATAGTCAG
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--gtttctttcctttacgtgttcatggcttaattaatccattttcatggactcgatataaattttacacttacctttacaaaatactgcttgttctttccagAAACTTCCACATGATGCATATCAACTTCTTGCAGTGCCCCCTCCTATAAGTGGCATTCTTGTGATCTGTGCAAATTCAATCCATTATCATAGTCAG
upper sequence: AT5G51660.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G32890.1 (Glycine max), 3'ss of exon 5
-aaatttcctaaaataacaagctatttcatgactgaaatagttacttcggcaaacgttagtccctgatcatacttattcccattcttttggtatt-----ttccagAATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGAGGTGTTCTTGTGTTGTGTGCAAATACAATCCATTATCATAGTCAG
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tgtatctctcaagtccagcatct-tttaacttctga-----ttatttcccccctttttttcgctttaaactgtttttttaaattcgtgtcgtattcattttgtcagAATCTTCCCCATGATGCGTACAAGCTTCTTGCAGTGCCCTCGCCAATAGGTGGTGTTCTTGTAATTAGTGCTAACACTATTCATTATCACAGTCAGMapped 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|116380073|gb|EG422665.1|EG422665EST: TTAGTATCAATTCGACATTAAAACAACACCCAGTCATCTGGTCAGCTATT AATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGA
genomic: TTAGTATCAATTCGACATTAAAACAACACCCAGTCATCTGGTCAGCTATTgtatgttcgt ... tattttccagAATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcggcaaacgttagtccctgatcatacttattcccattcttttggtattttccagAATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGAGGTGTTCTTGTGTTGTGTGCAAATACAATCCATTATCATAGTCAG
ccctgat putative branch site (score: 4)
tattttcc putative PPT
atacttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatttcctaaaataacaagctatttcatgactgaaatagttacttcggcaaacgttagtccctgatcatacttattcccattcttttggtattttccagAATCTGCCCCATGATGCCTACAAACTACTTGCAGTACCATCTCCGATCGGAGGTGTTCTTGTGTTGTGTGCAAATACAATCCATTATCATAGTCAG
- - - - -aaaataa
- - - - - - - - caagcta
- - - - - - - - - - - - - - - -ctgaaat
- - - - - - - - - - - - - - - - - - - - - - - - gcaaacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatca