Sequence
atgc intronic sequence ATGC exonic sequenceTGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCACAGgttggtttctcctgtttcacacgttaatgcagtcataattattttggtgtcgaagcctcaacacccatattttaacttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40200.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 5'ss of exon 6
TGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCACAGgttggtttctcctgtttcacacgttaatgcagtcata--attattttggtgtcgaagcctcaacacccatattttaa-cttgcag----------------------------------------------------
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TGGAAAAGACTATGAGTATGATGCCCCTGTCAAGTTGTTGGACAAGCACTTACATGCAATGGCTCAATCACCTGACGAGCAGCTTGTGGTGGTGTCACAGgtctcaagttctttctgtactaacctatgtttttatgttataaatgagatggctaacctttcttgcttttatttagagcttggtatttattatttcatcatatgacaattttttgaaaaaaaatgatgaattttcag
upper sequence: AT5G40200.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: AC212112.4_FGT002 (Zea mays), 5'ss of exon 6
TGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCACAGgtt---ggtttctcctgtttcacacgttaatgca-gtcataattattttggtgtcgaagcctcaacacccatattttaacttgcag--------------------------------------------------
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TGGAAAAGATTATGAATATGATGCACCTGTCAAGTTGTTGGTGAAACATTTACATGCGATGGCGGAATCACCTGATGAACAGCTAGTGGTGGTATCACAGgtctgaagttcttcacatattaactttgaatgaataactctgtaatattattcatttagttttgtttttcataact-agctagtgtcttctttaaatttataacttgattgtacccgttgcattgaacctgtgcagMapped 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|163990706|gb|ES029174.1|ES029174EST: TTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCACAG GTTCTTGTTTCTGACATTAACATTGGTTATGAAGAGATT
genomic: TTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCACAGgttggtttct ... taacttgcagGTTCTTGTTTCTGACATTAACATTGGTTATGAAGAGATT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCACAGgttggtttctcctgtttcacacgttaatgcagtcataattattttggtgtcgaagcctcaacacccatattttaacttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT