Sequence
atgc intronic sequence ATGC exonic sequence...agccttgatatttaatccaaccaaacataggacaagaaagtttgagtacagtttgtgaaatgttgaatcttataatggtgaatcttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G17640.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G17640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g04140.1 (Oryza sativa), 3'ss of exon 1
-agccttga--tatttaatccaaccaaacataggacaagaaagtttgagtacagtt-tgtgaaatgttgaatcttataatggtgaatcttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
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taaacatgagctacatcatacgtggttaaatatgactttatggttt---tttatttatgatagagctttagttttatattgttgcctcttatactgt-tcacagGCAGAGAAGGAACCTATTTTAAGTAGCTTCTTGTACGCCAGCGTACTATCTCATGACTGTCTCGAGAGGGCGTTGAGTTTCGTCCTTGCAAACAGGCTCG
upper sequence: AT2G17640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G048740_T03 (Zea mays), 3'ss of exon 1
agccttgatatttaatccaaccaaacataggacaagaaagtttgagtacagtttgtgaaatgttgaatcttataatggtgaatc--ttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
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-gtctcacctctttatgcatggtcatgtttgtcatagttttactgttata-ttggtaaactgatggccggcagtgtgatggactgatggtcatgctccacagGCAGAAAAGGAACCTATTTTGAGTAGCTTCTTGTATGCCAGTGTGCTGTCTCATGATTGCCTAGAGCGTGCATTGAGCTTCGTCCTTGCAAATAGGCTTG
upper sequence: AT2G17640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G08930.1 (Glycine max), 3'ss of exon 1
agccttgatatttaatccaaccaaacataggacaagaaagtttgag-tacagtttg--tgaaatgttgaatcttat-aatggtgaatcttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
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-aacgggaatttgaaccttgttcaccacgttgtagtagactaggcccttctgttagacccaattctcaattgttattactgattgatggtgttatgtg---cagGCGGAGAAGGAGCCGATTCTGAGTAGCTTCTTGTACGCTAGCATTTTGGCGCATGATTGCTTGGAGCAAGCATTGGCGTTTGTCGCCGCTAATCGTCTCC
upper sequence: AT2G17640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G22630.1 (Glycine max), 3'ss of exon 2
--agccttgatatttaat--ccaaccaaacataggacaagaaagtttgagtacagtttgtgaaatgttgaatct-tataatggtgaatcttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
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tgaaatatgcagttagatgattcattttgcatatttgatgagtgttagagaacattt----acatgtttcatatgcatcatgatataccattatttgtgtg-cagGCAGAAAAGGAGCCAATTTTGAGTAGCTTCTTCTATGCCACTATTCTGTCTCATGATTGCTTGGAGCAAGCATTGGCTTTTGCTCTTGCCAACCGACTCC
upper sequence: AT2G17640.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0210g00190.t01 (Vitis vinifera), 3'ss of exon 1
agccttgatatttaatccaaccaaacataggacaagaaagtttg--agtacagtttgtgaaatgttgaatcttataatggtgaatcttgttgtgc---gtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
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ggtggtggtgtcggggt-gttgggctggaagagaatttcgtttggaagaataatttgt----tatctgatcttgacatatttgttgctaccatgcaatgtttcagGCGGAGAAGGAGCCAATTCTAAGTAGCTTCTTGTATGCCAGTATTTTGTCCCATGACTGTTTAGAGCAAGCATTGGCATTTGTTCTTGCAAATCGACTTCMapped 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|86016772|gb|DR312518.1|DR312518EST: CTCGTTCTGATCCTATTTGGGATGCTATAAGAGAAGAAGCTAAACTTGAG GCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCA
genomic: CTCGTTCTGATCCTATTTGGGATGCTATAAGAGAAGAAGCTAAACTTGAGgtttccctca ... tgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCA
EST:
gi|86016773|gb|DR312519.1|DR312519EST: CTCGTTCTGATCCTATTTGGGATGCTATAAGAGAAGAAGCTAAACTTGAG GCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCA
genomic: CTCGTTCTGATCCTATTTGGGATGCTATAAGAGAAGAAGCTAAACTTGAGgtttccctca ... tgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtacagtttgtgaaatgttgaatcttataatggtgaatcttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
ttgaatcttataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agccttgatatttaatccaaccaaacataggacaagaaagtttgagtacagtttgtgaaatgttgaatcttataatggtgaatcttgttgtgcgtttcagGCAGAGAAAGAGCCTATTTTGAGTAGCTTCTTGTATGCTGGTATCTTAGCACATGATTGTTTAGAGCAAGCTTTAGGGTTTGTTCTAGCCAACCGTCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - ccaacca
- - - - - - - - - - - -aacatag
- - - - - - - - - - - - - - - - caagaaa
- - - - - - - - - - - - - - - - - - - - - - - - -agtttgt