Sequence
atgc intronic sequence ATGC exonic sequencegtaacttcaaaagacactggtcaatgtataatctttttagccatgtgtttgactgtttcattttggtgatcatttcagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTCTTGCAAATGGATGGTGAGCCATGGAAGCAACCAATGAGCACTGAGTACT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18730.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 13
----------------gtaacttcaaaag-----acactggtcaatgtataatctttttagccatgtgtttgactgtttcattttggtgatcattt-cagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTCTTGCAAATGGATGGTGAGCCATGGAAGCAACCAATGAGCACTGAGTACT
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tcagtttagataaacagctactttgcaaattacaactccagatggcattcgacactgatatcctcaaaattatttaagcgacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT
upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G073380_T01 (Zea mays), 3'ss of exon 5
-----------------------gtaacttcaaaagacactggtcaatgtataa----tctttttagccatgtgtttgactgtttcat--tttggtgatcat-ttcagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTCTTGCAAATGGATGGTGAGCCATGGAAGCAACCAATGAGCACTGAGTACT
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gtaacttgctcccccaaacaaaaacaaaaaaaaagtattctataaactatagaaagaatatttattacttcattcagaagcaccgcataatttggtgctaatgttcagGCAGCGGCAATACGGATAGAGATCAAAGGTGGGTATTGGCACGACGCGTTCATGCAAATGGACGGGGAGCCATGGAAGCAACCACTTAGCTCCGAGTATT
upper sequence: AT2G18730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G22370.1 (Glycine max), 3'ss of exon 4
-------------------gtaacttcaaaagacactggtcaatgt-ataatctttttagccatgtgtttgactgtttcattttggtgatc--atttcagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTCTTGCAAATGGATGGTGAGCCATGGAAGCAACCAATGAGCACTGAGTACT
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aactttgatcagaactattattattgttataaatatatacgactgttatcattagcatcatttggcatgtgtgaaattgaatgtagaggtctaattttagGCAACAGCTATTCGATTGGAAGTCAGAGGTGGTGAATGGAAAGATGCATTTATGCAAATGGATGGAGAACCGTGGAAACAACCAATGAGCAAGGACTTCTMapped 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|164102921|gb|ES067894.1|ES067894EST: AAGCACATAGCTCAG GCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTC
genomic: AAGCACATAGCTCAGgtaacttcaa ... atcatttcagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtataatctttttagccatgtgtttgactgtttcattttggtgatcatttcagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTCTTGCAAATGGATGGTGAGCCATGGAAGCAACCAATGAGCACTGAGTACT
gtttgac putative branch site (score: 4)
tcatttc putative PPT
taatcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacttcaaaagacactggtcaatgtataatctttttagccatgtgtttgactgtttcattttggtgatcatttcagGCTGCTGCGGTAAGATTTGAGCTAAGAGGAGGTGACTGGAGAGACGCATTCTTGCAAATGGATGGTGAGCCATGGAAGCAACCAATGAGCACTGAGTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA