Sequence
atgc intronic sequence ATGC exonic sequencegtacggattctaatgatatttgtgattacacaaaggctttatcttttaaacatactcgtatatatagttttacatgtggtatttgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G60100.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 5
gtacggattctaatgatatttgtgattacacaaaggctttatcttttaaacatactcgtatatatagttttacat-----gtggtatttgtg-aagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
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----gtatgcttttggtatt---gattatttatggattgtttctcaagggtgtcctttattgattggtctaaaatcttaaatggtgtttatccaagGTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G063851_T02 (Zea mays), 3'ss of exon 5
gtacgg-attctaatgat-atttgtgattacacaaaggctttatcttttaaacatactcgtatatat------agttttacatgtggtatttgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
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gtatgatatattgcttatcaattgtctatggatagttttgttgcttttatagcatatactaacttatcctgggaaattcctgaatgatgttcctccagGTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G064023_T04 (Zea mays), 3'ss of exon 5
-------gtacggatt-ctaatgatatttg--tgattacacaaaggctttatcttttaaacatactcgt-atatatagttttacatgtggtatttgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
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gtataatatactgcttattagttgcctatggatagttatgttgcttttctagagcatatattaactcatcatgtgaaaatcctta-ataatgttcctgcagGTCCTTGGTGGAATGAGAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G42300.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------------------------gtacggattctaatgatatttgtg--attacacaaaggctttatctttta--aacatactcgt----------atatatagttttacatgtggtatt-tgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
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gtaattatattatccttttgtagatatatatctcttaaagttactagttgcattaaaagttgtcttcttctcttgtcatgtagatatatatcttttaaagttactagtggcattaagagttgtcttcttctcttgtcaataagcttgtgatttaacttatattttgagtaacctctgtcacaatttaaagGTACTTGGTGGAATGAGAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 5
-------------------------gtacggattctaatgatatttgtgattacacaaaggctttatcttt--taaacatactcgtatatatagttttacatgtggtatt-----------tgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
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gtaattatatcatccctttgtggatatatatcttttaa-attactagtggtaattaaaagctgtcttctttggtcaataagcttgtgatttaacttttattttgagtaacttccgttacaatttaaagGTACTTGGTGGAATGAGAGGAATGACAGCTTTAGTATGGCTAGGCTCAGCTGTTGACCCGGATGAG
upper sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 5
----------gtacggattctaatgatatttgtgattacacaaaggctt--tatcttttaaacatactcgtatatatagttttaca------------tgtggtatttgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
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gtaatgatagtctctgtttattctgatgtttgtaagtttacaatcttagagcaacacgtacatatattacagtgtgtaacctctcactgagttatcactgtcacaattgcaaagGTACTTGGTGGAATGAGAGGAATGACAGGGTTGCTGTGGGAAACCTCGTTGCTTGACCCAGATGAAMapped 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|86074093|gb|DR369850.1|DR369850EST: TGAAATCAGAACATGGAAAGGTTCCAGTGGGGAACATCACCGTTGATATG GTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTG
genomic: TGAAATCAGAACAAGGAAAGGTTCCAGTGGGGAACATCACCGTTGATATGgtacggattc ... atttgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttatcttttaaacatactcgtatatatagttttacatgtggtatttgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
tatatatagttttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggattctaatgatatttgtgattacacaaaggctttatcttttaaacatactcgtatatatagttttacatgtggtatttgtgaagGTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG