Sequence
atgc intronic sequence ATGC exonic sequencegtatttctcttttcttcttcttcctccattgttactctgtttttcgacaatgcttcattgttttaaaagaccacatcttttcttaacacagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45800.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G46460.1 (Glycine max), 3'ss of exon 1
gtatttctcttttcttcttcttcctccattgtta---ctctgtttttcgacaatgcttc---att--gttttaaaagaccacatcttttcttaacac-agATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
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gtattttgatatggtttgattcaaggaaagaagaaatatatgtagtttaaaattgtttctaaatttggtgctaatggtgcaatgttattttggtcaccagATGAACACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
upper sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G08020.1 (Glycine max), 3'ss of exon 1
---gtatttctcttttcttcttcttcctccattgttactctgtttttcgacaatgcttc-------attgttttaaaagaccacatcttttcttaacacagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
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gattaaattcttttcaatacaaaataagttaagattaaatt-cctttaaatattgttcctaaatcgagggtgccaatgatatactacttaatgttggtcagATGTGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTCG------
upper sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G39740.1 (Glycine max), 3'ss of exon 1
----gtatttctcttttcttcttcttcctccatt---gttactctgtttttcgacaatgcttcattgttttaaaagaccacatcttttcttaac--acagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
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tttgatatggtttgatacaatgaaagaagacatttatgtagtttaaacttgttccaaactttggcgctaatggtgcaatatattttattttggttatcagATGAGCACCTACTCCTCAATGGATGGTGTCCTCTATTGCAAGCCACACTTTGAACAACTTTTCAAGGAATCTGGCAATTTCAGCAAGAACTTTCAAACAG
upper sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01590.1 (Glycine max), 3'ss of exon 1
---gtatttctcttttcttcttcttcctccattgttactctgtttttcgacaatgcttcattgttttaaaagaccac--atctttt-cttaaca-----cagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
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gaagtaaattgatatgatactattcattcaaataaaatgtcatttt--aacattgttcctaaattcgggggtgccaatgatatactacttaatgttggtcagATGAGCACATACTCCTCAATGGATGGAATTCTTTATTGCAAGACACATTTTGAACAGCTTTTCAAGGAATCTGGAAATTTCAGCAAGAACTTTG------
upper sequence: AT2G45800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g03370.t01 (Vitis vinifera), 3'ss of exon 1
-----------------gtatttctcttttcttcttcttcctccattgttactctgtttttcga-caatgctt-cattgttttaaaagacc--acatcttttcttaac---acagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
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gtatgtttcttctaagcctatttttcccctgtttttttttttttttggtaaatttttacgaaaatcaatatctacgtaaatttatgagatataacaagtgggttttactttgcagATGAGCAACTACTCATCCATGGATGGGGTCCTCTACTGCAAACCTCATTTTGAGCAGCTGTTCAAGGAGTCTGGCAATTTCAGCAAGAATTTTCAAACATMapped 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|19878067|gb|AU238898.1|AU238898EST: CTTATCACAAATCATGTTTCAGATGCACCCATTGCAAAGGCACTCTCGTG ATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTC
genomic: CTTATCACAAATCATGTTTCAGATGCACCCATTGCAAAGGCACTCTCGTGgtatttctct ... cttaacacagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtttttcgacaatgcttcattgttttaaaagaccacatcttttcttaacacagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
tcttaac putative branch site (score: 2)
ccacatcttttctt CT-rich tract
ttcattgttttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttctcttttcttcttcttcctccattgttactctgtttttcgacaatgcttcattgttttaaaagaccacatcttttcttaacacagATAAGCAATTACTCATCAATGGATGGAGTTCTTTACTGTAAGCCACACTTCGAACAGCTTTTCAAAGAATCTGGCAATTACAGCAAGAATTTTCAGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA