Sequence
atgc intronic sequence ATGC exonic sequencegtaagtccttctatatgagatatattgcatagaactcaattcctagctccaaccttaaaatctaagagatctctgacctgtataaaaagcattttgaaaacctattttccgtgtttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G48640.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G48640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 3'ss of exon 6
gtaagtccttctatatgagatatattgcatagaactcaattcctagctccaaccttaaaatctaagagatctctgacctgtataaaaagcattttgaaaacctattttccgtgtttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAG
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----------------caaatgaattgaattgt-ctttattatgattagtgaacataatgcacgcaaaattttcaactataccttttcctatgcttatcatctgctgttact--tgcagGGGAATTGTCAATGATACTTACAAGATGGATCTTATTCTCATACACCCACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGAC
upper sequence: AT5G48640.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G408242_T03 (Zea mays), 3'ss of exon 7
gtaagtccttctatatgagatatattgcatagaactcaattcctagctccaaccttaaaatctaagagatctctgacctgtataaaaagcattttgaaaacctattttccgtg--tttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAG
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-------tctaattatgggtgataatgtatg---ctcagtcttcagct--attcctgttgcct----gttgttacatctttttttaaagaa-----aaaactgaccttatgtgacttgcagGGGCCTTGTTAATGATACATACAAGATGGACCTTATCCTCATATACCCTCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATMapped 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|125136449|gb|EL176479.1|EL176479EST: TTTTTGCAAGATGCTGCATTAAACGATGTAAATATGAACCAGATTACATG GGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCC
genomic: TTTTTGCAAGATGCTGCATTAAACGATGTAAATATGAACCAGATTACATGgtaagtcctt ... cgtgtttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagatctctgacctgtataaaaagcattttgaaaacctattttccgtgtttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAG
ctctgac putative branch site (score: 3)
cctattttcc putative PPT
tataaaaagcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtccttctatatgagatatattgcatagaactcaattcctagctccaaccttaaaatctaagagatctctgacctgtataaaaagcattttgaaaacctattttccgtgtttcagGGGAATTGTTAATGATACTTATAAGATGGACCTCATTCTTGTACACCCTCCCTACCGCATAGCGCTAGCATGCATATACATAGCAAGTGTCCACAGAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG