Sequence
atgc intronic sequence ATGC exonic sequenceATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGgtttgttttacaaatcttgcttctgattttactaacatggatcggtataaatagatagaattgataatgatctacattgagaatagatagtctttgattatgctctcaattcaattctag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03540.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 2
ATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGgtttgttttacaaatcttgcttctgattttactaacatggatcggtataaatagatagaattgataatgatctacattgagaatagatagtctttgattatgctctcaattcaattctag
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ATTAGAACTCACTCTATTAGGAAGGCTCATGAGAATATTGATAGGACTTTGAAGGCTGCGGAGGTTATATTGGCTCACTTCGATCAATATCGTCAGgttggttttg----------ttttggtgctaccgtgatccgtttctcataatgtgtcttattttttattatttaaattaagt-----tgctctttgttgaattgatgaattgaaa-----
upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 2
ATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGgtttgttttaca--aatcttgct----tctgattttactaacatggatcggtataaatagatag--aattgataatgatctacattgagaatagatagtctttgattatgctctcaattcaattctag
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ATTAGAACTCACTCTATTAGGAAGGCTCATGAGAATATTGATAGGACTTCGAAGGTTGCGGAGGTTATATTGGCTCACTTCGATCAATATCGTCAGgttggttttgtgttggtcctaccgtgatccgtttctcataatgtagctttttttttttaattattcaaatgaagttgctctttgttga--attgataaattg--------------------------
upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 2
ATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGgtttgttttacaaatcttgcttctgattttactaacatggatcggtataaatagatagaattgataatgatctacattgagaatagatagtctttgattatgctctcaattcaattctag
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ATCAGAACGCATTCTATTCGGAAAGCCCATGAGAATATTGATAGGACTTTGAAGTCTGCAGAGGCCATATTGGCTCACTTTGATCAATATTATCAGgttcgttctt---gtggtggttaccattgttcgctgtttgatt--tttgaatc-----acttcatgacctgcttcactctaaactgat--tttttctttcttcttcttcttt--------
upper sequence: AT5G03540.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 2
ATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGgtttgttttacaaatcttgctt--ctgattttactaacatggatcggtataaatagatagaattgata-atgatctacattgagaatagatagtctttgattatgctctcaattcaattctag
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ATTAGAACGCATTCTATTCGAAGAGCTCATGAGAATATTGACAAGACTTTGAAGGCTGCCGAGGTTATATTGGCTCAATTCGACCTTTATCGTCAGgttggattttcagtaggcacttaattggttcaatttaccgagattattattatctggtggattccctgcatgaacttcatagtttattcaatgttgttgt-----------------------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|301502195|gb|HO207735.1|HO207735EST: CTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAG GCAGAGACTAAAGTACTCAAGGGGCCACATGAGGACCTGGAAAGTTATCTG
genomic: CTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGgtttgtttta ... tcaattctagGCAGAGACTAAAGTACTCAAGGGGCCACATGAGGACCTGGAAAGTTATCTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTAGGACTCATGCTATAAGGAAAGCTCATGAGAATATTGATAGGACTCTTAAGGCTGCTGAAGTTATTTTGTCTCAATTCGATCTCCTCCGTCAGgtttgttttacaaatcttgcttctgattttactaacatggatcggtataaatagatagaattgataatgatctacattgagaatagatagtctttgattatgctctcaattcaattctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC