Sequence
atgc intronic sequence ATGC exonic sequencegtaatttttagaaaagtgtcaatctttgagctgattctgtgtgttggaatagttaggattgggtgttgatttagtttacgtagtaaagggcaattagaaagatgtttcttttgagtttagtgttgttgtggtggtttcttacaaatggattttcttgtgttgttgttgtttatacagGAGTGTTTTATTTATATATGAAGACTATTGAGAGAGCTCACATGCCAAATAAATTGTGGGAGAGAGTTAAGCTGCCTGTAAACTATGAGAAGGCTCTTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23280.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0030g01480.t01 (Vitis vinifera), 3'ss of exon 12
gtaatttttagaaaagtgtcaatctttgagctgattctgtgtgttggaatagttaggattgggtgttgatttagtttacgtagtaaagggcaattagaaagatgtttcttttgagtttagtgttgt-tgtggtggtttcttacaaatggattttcttgtgttgttgttgtttatacagGAGTGTTTTATTTATATATGAAGACTATTGAGAGAGCTCACATGCCAAATAAATTGTGGGAGAGAGTTAAGCTGCCTGTAAACTATGAGAAGGCTCTTGA
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---------------------------------------------------------------------tgtgatttatggattgtttcctctttattaa-atttagttctttagatcaaagctgtatgtggctgactat-gttaatgattggtctc-------tggttcttgtgcagGAGTGTTTTATCTATACATGAAAACCATTGAAAGAGCCCATATGCCAAACAAATTATGGGAACGGGTTAAATTGCCACGAAACTACGGAAAGGCTCTTGA
upper sequence: AT1G23280.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g09220.t01 (Vitis vinifera), 3'ss of exon 3
gtaatttttagaaaagtgtcaatctttgagctgattctgtgtgttggaatagttaggattgggtgttgatttagtttacgtagtaaagggcaattagaaagatgtttcttttgagtttagtgttgt-tgtggtggtttcttacaaatggattttcttgtgttgttgttgtttatacagGAGTGTTTTATTTATATATGAAGACTATTGAGAGAGCTCACATGCCAAATAAATTGTGGGAGAGAGTTAAGCTGCCTGTAAACTATGAGAAGGCTCTTGA
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---------------------------------------------------------------------tgtgatttatggattgtttcctctttattaaaat-tacttctttagatcaaagctgtatgtggctgactat-gttagtgattggtctc-------tggttcttgtgcagGAGTGTTTTATCTATACATGAAAACCATTGAAAGAGCCCATATGCCAAACAAATTATGGGAACGGGTTAAATTGCCACGAAACTACGGAAAGGCTCTTGAMapped 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|164202021|gb|ES097949.1|ES097949EST: CTCTTGCCCTCTTGCTAATAGCCGATACGCCACTATCCGTGACCATGATG GAGTGTTTTTATTTANATATGAAGACTA
genomic: CTCTTGCCCTCTTGCTAATAGCCGATACGCCACTATCCGTGACCATGATGgtaattttta ... gtttatacagGAGTGTTTT-ATTTATATATGAAGACTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgtggtggtttcttacaaatggattttcttgtgttgttgttgtttatacagGAGTGTTTTATTTATATATGAAGACTATTGAGAGAGCTCACATGCCAAATAAATTGTGGGAGAGAGTTAAGCTGCCTGTAAACTATGAGAAGGCTCTTGA
ttcttac putative branch site (score: 2)
ttgtttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttttagaaaagtgtcaatctttgagctgattctgtgtgttggaatagttaggattgggtgttgatttagtttacgtagtaaagggcaattagaaagatgtttcttttgagtttagtgttgttgtggtggtttcttacaaatggattttcttgtgttgttgttgtttatacagGAGTGTTTTATTTATATATGAAGACTATTGAGAGAGCTCACATGCCAAATAAATTGTGGGAGAGAGTTAAGCTGCCTGTAAACTATGAGAAGGCTCTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC