Sequence
atgc intronic sequence ATGC exonic sequencegtatttatagtcttctctttgtttgtgcaaggaatcctgtattttttgtagtgttagaacaagttgttcgtttgttttttcaacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12520.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12520.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 4
--------------gtatttatagtcttctctttgtttgtgcaaggaatcctg-tattttttgtagtgttagaacaagttgttcgtttgttttttcaacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
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aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttattta---cagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
upper sequence: AT3G12520.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
-----gtatttatagtctt--ctctttgtttgtgcaaggaatcctgtattttttgtagtgttagaacaagt--tgttcgtttgttttttcaacc---cagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
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tatatgattctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
upper sequence: AT3G12520.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G10590.1 (Glycine max), 3'ss of exon 3
gtat-ttatagtcttctctttgtttgtgcaaggaatcctgtattttttgtag-------tgttagaacaagttg--ttcgtttgtttttt---caacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
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-tatatgattctgctggctcagcactcagcatcaaacctgaattttttatgaaagggattttaaggataacctacatatacttgttttttggtcatttcagGCTTGGATGGCTTATTCGTTTCATTAGCCATTCAGTGATATCTGGCTTTACAACCGCTTCAGCTATTGTCATTGGTTTATCTCAAGCAAAATACTTCTTG
upper sequence: AT3G12520.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g00010.t01 (Vitis vinifera), 3'ss of exon 3
----gtatttatagtcttctctttgtttgtgcaagga--atcctgtattttttgtagtgtta------gaacaagttgttcgtttgttttttcaacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
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atttgtactagaaatttgcatattttctatcttttaattattctcaaatttctgtgatgtcatttagaaagaaaatgatgcacccttttttcctttctagGCTTGGATGGCTTATTCGTTTCATCAGTCACTCTGTGATTTCTGGGTTTACGACAGCTTCAGCAATTGTGATTGCCTTATCTCAAGCAAAGTATTTCCTGMapped 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|19877624|gb|AU238455.1|AU238455EST: TTGTTGGCTCTTATGGTCGGAATATTTGAGAGCATTATGGGGTTCTTGAG GCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTAC
genomic: TTGTTGGCTCTTATGGTCGGAATATTTGAGAGCATTATGGGGTTCTTGAGgtatttatag ... ttcaacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcctgtattttttgtagtgttagaacaagttgttcgtttgttttttcaacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
ttcgtttgttttttc CT-rich tract
tattttttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttatagtcttctctttgtttgtgcaaggaatcctgtattttttgtagtgttagaacaagttgttcgtttgttttttcaacccagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT