Sequence
atgc intronic sequence ATGC exonic sequenceTCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtttttcctctagtttcgttaaccagagtgtatgtcaattttaattcatcttctccactatatacggccattgaattgattaacttctgtatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54440.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g72340.1 (Oryza sativa), 5'ss of exon 6
TCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtttttcctctagtttcgttaaccagagtgtatgtcaattttaattcatcttctccactatatacggcca-ttgaattgattaacttctgtatgcag---
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TCAAGTGATGAGGTGGAGTGACGGTTCCTATCTTGAAGACCAGGACCATTGGTGGCTATCTGGTATTCACAGGGATGTTCTACTAGTATCAAAGCCACAGgttacttctctagttttgctcatgcaatattgaacgaattctttcccttttgcaatgaagtgaatggttagctgagcttatgacattttcttcgtctcag
upper sequence: AT3G54440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA13G26700.1 (Glycine max), 5'ss of exon 5
TCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtt---tttcctctagtttcgttaaccagagtgtatgtcaattttaattcatcttctccactatatacggccattgaattgattaacttctgtatgcag----
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TCAAGTGTTTAGATGGTGTGATGGTTCTTACCTTGAAGACCAGGACCAATGGAGGTTATCTGGTATCCACCGTGATGTTCTTCTTATGGCAAAGCCGGAGgttagttttctccaaatttctcctcacctactattgctttatattg-tttacgagaagcattct-tattagagttatgttagtgcgcatc-ataaaaggtcaa
upper sequence: AT3G54440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv13s0067g03000.t01 (Vitis vinifera), 5'ss of exon 5
TCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtt----tttcctctagtttcgttaaccagagtgtatgtcaattttaattcatcttctccactatatacggccattgaattgattaacttctgtatg-cag--
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TCAAGTATTTAGATGGAGTGATGGCTCTTACCTTGAAGATCAAGATCAATGGTGGTTATCCGGTATTCATCGAGACGTGCTTCTTTTAGCCAAGCCACAGgttagcattctctttagttttgtct-tcattccctg-gcctctcaaaattaaactacattaatgtgca-gtaaatagcataggtagagactcctatgataggt
upper sequence: AT3G54440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ11904 (Selaginella moellendorffii), 5'ss of exon 5
TCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtttttcctctagtttcgttaaccagagtgtatgtca-attttaattcatcttctccactatatacggccattgaattgattaacttctgtatgcag
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TCAAGTGATGCGGTGGAGTGATGGATCGTATCTTGAAGACCAAGACCACTGGTGGCTATCTGGGATTCACCGAGATGTGATACTGTTTTCAAAGCCGCAAgtaagtacttggtcggtgtttgttctaacatgggccgtgttataatgtgggattgttttgatag---------------------------------
upper sequence: AT3G54440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ13378 (Selaginella moellendorffii), 5'ss of exon 5
TCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtttttcctctagtttcgttaaccagagtgtatgtca-attttaattcatcttctccactatatacggccattgaattgattaacttctgtatgcag
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TCAAGTGATGCGATGGAGTGATGGATCGTATCTTGAAGACCAAGACCACTGGTGGCTATCTGGGATTCACCGAGATGTGATACTGTTTTCAAAGCCGCAAgtaagtacttggtcggtgtttgttctaacatgggccatattataatgtgggattgttttgatag---------------------------------Mapped 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|125281967|gb|EL296052.1|EL296052EST: GGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAG GTCTTCATTGCTGACTACTTTTTTCAAGTCAAAA
genomic: GGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtttttcctc ... ctgtatgcagGTCTTCATTGCTGACTACTTTTT-CAAGTCAAAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCAAGTCTTTAGATGGAGTGATGGTTCATACCTTGAAGACCAAGATCATTGGTGGTTGTCTGGTATTCATCGAGATGTGCTTTTGTTAGCAAAGCCCAAGgtttttcctctagtttcgttaaccagagtgtatgtcaattttaattcatcttctccactatatacggccattgaattgattaacttctgtatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG