Sequence
atgc intronic sequence ATGC exonic sequencegtatctttctcatggttttggtttctttttcaaattgaaataagatatggatcatagtatttgcattgcctgaagccttatgataacttattggtatatctcatgtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G32980.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 2
-gtatctttctcatggttttggtttctttttcaaattgaaataagatatggatcatagtatttgcattgcctgaagccttatgataacttattggtatatctcatgtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
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gttagccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctga--cataagtaaaaccaattccttcttttgatgttat---tttaacttgtatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
upper sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G28950.2 (Glycine max), 3'ss of exon 3
-gtatctttctcatggttttggtttctttttca--aattgaaataagatatggatcatagtatttgcattgcctgaagccttatgataacttattggtatatctcatgtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
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gttagccttttagccattccagttgtatctggaccatctgacgtttactagttggctaagaatta--attttctga--cataagtaaaaccaatgccttcttttgatgttat--tttaacttatat-ctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
upper sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 2
gtatctttctcatggttttggtttctttttcaaattgaaataagatatggatcatagtatttgcattgcctgaagccttatgataacttattggtatatctcatgtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
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------------------------------------------------caaggataattttttggtctctttta--cttgaatctgtttatttgaaaattttatactg-ggcacttcctaactgacatgt-------ttgttgaattggattgttt-agGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAGTGTGAGACTTTAGCAAGGATTACTGCTATATTGAAAGATGTTATTCAAAMapped 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|164094922|gb|ES059619.1|ES059619EST: TTGTTCAAAGGAAAATTGCAGACTTGCAGGTCGAGCTTCAAGGGAGGAAG GATGATAAAAATGTGGCGCATTTGACTCATG
genomic: TTGTTCAAAGGAAAATTGCAGACTTGCAGGTCGAGCTTCAAGGGAGGAAGgtatctttct ... cgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATG
EST:
gi|116457559|gb|EG500151.1|EG500151EST: TTGTTCAAAGGAAAATTGCAGACTTGCAGGTCGAGCTTCAAGGGAGGAAG GATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAA
genomic: TTGTTCAAAGGAAAATTGCAGACTTGCAGGTCGAGCTTCAAGGGAGGAAGgtatctttct ... cgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
atataac putative branch site (score: 3)
tatataacttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctttctcatggttttggtttctttttcaaattgaaataagatatggatcatagtatttgcattgcctgaagccttatgataacttattggtatatctcatgtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG