Sequence
atgc intronic sequence ATGC exonic sequenceCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGCAGgtaaaaagtttgatctgactcctaacacagatgtggctaggctattaagtttaaaagagctttaactgcctcttgttataggtcgttactcgccttccat...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G55020.1 |
intron # | 15 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: LOC_Os01g61860.2 (Oryza sativa), 5'ss of exon 15
CTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGCAGgtaaaaagtttgatctgactcctaacacagatgtggctaggctattaagtttaaaagagctttaactgcctcttgttat-aggtcgttactcgccttccat-----
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CCTGATGCGTGTAGAGCAAGAACAGAAAGTCACTGAGGATGCGCGCATATTCGCTGAGCAAGATGCTGCTGCTCAGAAATATGCTGCACATGTGCTCCAGgtta---gtttaatttcatcgattatctatgtactg-tatttttttctgttctaatg--cttatgtcatgttgaaacatgaaatggtcattcttttcttgattgca
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA20G38810.1 (Glycine max), 5'ss of exon 15
CTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGCAGgtaaaaagtttg---atctgactcctaacacagatgtggctaggctattaa-gtttaaaagagctttaactgcctcttgttataggtcgttactcgccttccat
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CTTGATGCGGGTGGAGCAAGAGCAAAAGGTGACTGAGGATGCTCGTAGGTTTGCTGAGCAAGATGCAGCCGCACAAAGATATGCTGCGCAAGTCCTTCAGgttaccttttttcctttttttcaccttgtattgctcttgtatgttggttaatatctgtcacatatacaagataatcatgttaaaaaagcatcgttgtttt----
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: GLYMA10G44110.1 (Glycine max), 5'ss of exon 15
CTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGCAGgtaaaaagtttgatctgactcctaacacagatgtggctaggctattaagtttaaaagagctttaactgcc------tcttgttataggtcgttactcgccttccat
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CTTGATGCGGGTGGAGCAAGAGCAAAAGGTGACTGAGGATGCTCGTAGGTTTGCTGAGCAAGATGCAGCCGCACAAAGATATGCTGCGCAAGTCCTTCAGgttgcc--ttttcccttttttctcatcttg-tattgctcttgtatttcgttaatatcagtcacaaatacaagataatcatattaaaaaaaatcattgtttttc---
upper sequence: AT3G55020.1 (Arabidopsis thaliana), 5'ss of exon 15
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 5'ss of exon 15
CTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGCAGgtaaaaagtttgatctgactcctaacacagatgtggctaggctattaagtttaaaagagctttaactgcctcttgttataggtcgttactcgccttccat-
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ATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTCAGgttatttattt-atttatttaatgtctttggtatgccaaggtggacaatttctacattatgtcctatccttggagaattagttcataaatgaatttgcttaMapped 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|124764996|gb|EH855126.1|EH855126EST: GCTCAAGTCTTGCAG GAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCA
genomic: GCTCAAGTCTTGCAGgtaaaaagtt ... actggtctagGAAAAATACGAGGAAGCTGTTGCTGCACTGGCTGAAATGGAGAAGAGAGCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGCAGgtaaaaagtttgatctgactcctaacacagatgtggctaggctattaagtttaaaagagctttaactgcctcttgttataggtcgttactcgccttccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgactc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcgccttc