Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcttatatctatgtatatacatgatcgatatgtcatgtttgaacaaaatttagcactaatttgaagcatattttcatgaataatgacaataacaaacaatccgttttttttccagGGATTAACGATTGTAACTCATATTCTTAAAGAAGGTGGAAAATTTATTGCAAAGATATTCCGTGGAAAAGATACAAGTCTCTTGTACTGTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01230.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g49140.1 (Oryza sativa), 3'ss of exon 7
gtaagtttcttatatctatgtatatacatgatcgatatg-tcatgtttgaacaaaatttagcactaatttgaagcatattttcatgaataatgacaataacaaacaatccgttttttttccagGGATTAACGATTGTAACTCATATTCTTAAAGAAGGTGGAAAATTTATTGCAAAGATATTCCGTGGAAAAGATACAAGTCTCTTGTACTGTCAA
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--------------------tctttttgtgcttgttttggttatattttgccttattttatttttagttggttgggtagctt-atatatctggctgatgt--actcttttgtgttgtgtttagGCATTGACAATTGTGACTCACGTACTTAAAGTTGGTGGGAAATTTGTTGCGAAGATTTTCCGTGGAAAAGATACAAGTCTGTTGTATTGCCAG
upper sequence: AT5G01230.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtttcttatatctatgtatatacatgatcgatatgtcatgtttgaacaaaatttagcactaatttgaagcatattttcatgaataatgacaataacaaacaatccgttttttttccagGGATTAACGATTGTAACTCATATTCTTAAAGAAGGTGGAAAATTTATTGCAAAGATATTCCGTGGAAAAGATACAAGTCTCTTGTACTGTCAA
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------------------tttgagagcaatgtataaatgttgcctggtaaccgatttgtttgtgaatgttgtttatgtttgtatta-cactgatattattggac---caacttattttgtagGGTTTAACAATTGTTACTCATGTGCTTAAAAAAGGTGGAAAATTTATTGCAAAGATATTTCGGGGAAAAGATACTAGTCTCCTTTATTGCCAGMapped 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|164117728|gb|ES112689.1|ES112689EST: GTCCAGTCCCAACTCATACTAGCA GGATTTAACGTATTGTAACTCATATTCTTAAAGAAGGTGGAAAATTTATTG
genomic: GTCCAGTCCCAACTCATACTAGCAgtaagtttct ... ttttttccagGGA-TTAACG-ATTGTAACTCATATTCTTAAAGAAGGTGGAAAATTTATTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgaagcatattttcatgaataatgacaataacaaacaatccgttttttttccagGGATTAACGATTGTAACTCATATTCTTAAAGAAGGTGGAAAATTTATTGCAAAGATATTCCGTGGAAAAGATACAAGTCTCTTGTACTGTCAA
caataac putative branch site (score: 2)
tccgttttttttcc putative PPT
atattttcatgaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcttatatctatgtatatacatgatcgatatgtcatgtttgaacaaaatttagcactaatttgaagcatattttcatgaataatgacaataacaaacaatccgttttttttccagGGATTAACGATTGTAACTCATATTCTTAAAGAAGGTGGAAAATTTATTGCAAAGATATTCCGTGGAAAAGATACAAGTCTCTTGTACTGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG