Sequence
atgc intronic sequence ATGC exonic sequence...gtctctttgttttgctagaggaagtaatctgttcaatagtttctgatgagtgtattgatggatatggaatgtgagaagtatgtggttttgtttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12590.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 3'ss of exon 2
-gtctctttgttttgctagaggaagtaatctgttcaatagttt-ctgatgagtgtattgatggatatggaatgtgagaagtatgtggtttt-gtttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC
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ctgctgaatgttttgattt-gatactaacatg--cattactccactaacgaatcgagtattatcttttgggtgttattttgacctttcttgagtacgctgtagGAAAACGGATTGCTTCATGTCCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACC
upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G014313_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------gtctctttgttttgctagaggaagtaat--ctgttca--atagtttctga---tgagtgtattgatggatatggaatgtgagaagtatgtggt----------tttgtttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC
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gtaattcaccaagtccagttaagaaaggatcaaggaaacgattaagcttaccatgtgcagtaacatgaatgccacgatgagtgtgatgatgcttagttattatgatttcaaacactgaatggactattccacatgacttctccagtgtatatcgtgtttacggtatctagtgactgtagGAAAATGGATTACTTCATGTTCCAAAGGAAGACGCGCAGAAGGCTCAGGCAGCCATGTTTTCTGATCCAAACATGGCCATGGACATGATGAAGAAGAACC
upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 3
--gtctctttgttttgctagaggaagtaatctgttcaatagtttctgatgagtgtat---tgatggatatgg-aatgtgagaagtatgtggttttgtttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC
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gaagttagtaactttgtcatgaga-----tttgtgcagtacttta-aatgatcttgtgcctgaccaattcaacagtgaactgattgtttgtgtctttccattgaagGAAAATGGTCTGTTGTTTGTTCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACC
upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 2
gtctctttgttttgctagaggaagtaatctgttcaa--tagtttctgatgag---tgtattgatggatatggaatgtgagaagtatgtggttttgtttg----ttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC
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--------ggtcttttgagggagtgcatacactgaagctagcttgcagtgtgccttctcttgtgggttattcta-atgccatttatgcacatttgcttgaccatggcagGAAAATGGATTACTGCATGTTCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCMapped 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|125081791|gb|EL142880.1|EL142880EST: CGGAGATTCTACTTCAGCAACGAG GAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCT
genomic: CGGAGATTCTACTTCAGCAACGAGgtaatgagtt ... tttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCT
EST:
gi|124904414|gb|EH978494.1|EH978494EST: TTATCCCGCCGAAATCATTCCGTGCTCGGAGATTCTACTTCAGCAACGAG GAGAATGGTTT
genomic: TTATCCCGCCGAAATCATTCCGTGCTCGGAGATTCTACTTCAGCAACGAGgtaatgagtt ... tttgttgtagGAGAATGGTTT
EST:
gi|124964219|gb|EL038501.1|EL038501EST: TTATCCCGCCGAAATCATTCCGTGCTCGGAGATTCTACTTCAGCAACGAG GAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAAT
genomic: TTATCCCGCCGAAATCATTCCGTGCTCGGAGATTCTACTTCAGCAACGAGgtaatgagtt ... tttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgagtgtattgatggatatggaatgtgagaagtatgtggttttgtttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC
tattgat putative branch site (score: 3)
ttttgttt putative PPT
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctttgttttgctagaggaagtaatctgttcaatagtttctgatgagtgtattgatggatatggaatgtgagaagtatgtggttttgtttgttgtagGAGAATGGTTTGCTACATGTTCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -tgttttg
- - - - - - - - - - gaagtaa
- - - - - - - - - - - - - - ctgttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttttg