Sequence
atgc intronic sequence ATGC exonic sequencegtacagtaaaatattcttccgtacttgttcgaacttaacataatttgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G45030.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g36780.1 (Oryza sativa), 3'ss of exon 10
-------------------gtacagtaaaatattcttcc----gtacttgt-tcgaacttaacataatttgcttctc----tggggatgaaattctgatattgtgtttgttgttgggtcaatt-----ttcctaaatca---gGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
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gtaaatttttgagtgaagtgtagggccacaggctattcaagaagtacctctgtccactatactaccatgtgctcttcgattttctgttgacattttcggatt-tgttctgtgttggtctgattatttgttctcgcatcaatagGTGATACATTTACAGATGGATCAGTGAAATATACCATGACTTCCATGAATGTCCCTGAACCTGTGATGTCCTTGGCTGTCTCCCCTATATCTAAAGATTC
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G056393_T02 (Zea mays), 3'ss of exon 10
gtacagtaaaatattcttccgtacttgttcgaacttaacataatttgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
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--------gtacgcagacaaacaaggggacaatcttactttattttatagttctgtttacttcattt--attctggatctgacttttcacttctctttgtcaat-agGCGATACATTTACGGATGGAACAGTGAAATATACTATGACTTCAATGAATGTCCCTGAACCTGTGATGTCCTTGGCAGTTTCACCTATATCTAAAGACTC
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G16460.1 (Glycine max), 3'ss of exon 10
gtacagtaaaatattcttccgtacttgttcgaacttaacataatt-tgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
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-----gtgttgt-tggggcagtctctttccattcattatttatttctgctcttatttttgtttcattttgattatatatgtgtt-taacatttgtcttggtca-tcagGAGATACTTTTACTGACGGTTCAGTTAAATACACAATGACTTCTATGAATGTTCCTGAGCCAGTGATGTCATTAGCTGTACAGCCAGTCTCTAAAGATTC
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA01G14800.1 (Glycine max), 3'ss of exon 5
gtacagtaaaatattcttccgtacttgttcgaacttaacataatttgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaa--atcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
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gt-tgttggggcagtctcttttcattcatt--atttatttctgctcatatttttg----tttcattttgattatacatat-ttgtttaa-catttgtcttggtcatcagGAGATACTTTTACTGACGGTTCAGTTAAATACACAATGACTTCTATGAATGTTCCTGAGCCAGTGATGTCATTAGCCGTACAGCCGGTTTCTAAAGATTC
upper sequence: AT2G45030.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv15s0021g02450.t01 (Vitis vinifera), 3'ss of exon 10
gtacagtaaaatattcttccgtacttgttcgaacttaacataatttgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
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------tgatgcttcattccaattttgcttatattgctctttgcttcatttgtttcatat-atatatatatatatttcatgatatctaaacttctttttgtcatcagGTGATACTTTTACTGATGGGTCAGTGAGATACACCATGACCTCTATGAATGTTCCAGAACCGGTCATGTCATTAGCTATTTCACCCGTTTCTAAGGATTCMapped 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|124881757|gb|EH960659.1|EH960659EST: GGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAG GTAATACATTTACGGATGGATCAGTC
genomic: GGCACACGCTGGACAAATTGTAGCTGTGTTTGGTATTGAGTGTGCATCAGgtacagtaaa ... cctaaatcagGTGATACATTTACGGATGGATCAGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
tcctaaa putative branch site (score: 2)
ttttcct CT-rich tract
atgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacagtaaaatattcttccgtacttgttcgaacttaacataatttgcttctctggggatgaaattctgatattgtgtttgttgttgggtcaattttcctaaatcagGTGATACATTTACGGATGGATCAGTCAAGTACACAATGACATCGATGAACGTTCCTGAACCTGTTATGTCCTTAGCTGTTCAACCAGTTTCAAAAGATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT