Sequence
atgc intronic sequence ATGC exonic sequence...cgcaacaataatctatataagaaaacctcactatgtttttctacacaagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13320.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
cgcaacaataatctatataagaaaacctcactatgtttttctaca-caagatattta-gttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
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-----------gtgatatcagtgatgcaaac-atgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
cgcaacaataatctatataagaaaacctc---actat-gtttttctacacaagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
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-taaaagataatcaacaaaatctattttctaggctattgttatagtagtagttttatttggtgtaaatgtgca--tctcagttctacctt-atcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 7
-----cgcaacaataatctatataagaaaacctcactatgtttttctacacaagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
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tttaatgctacaactaatgctgtggcagcattgtttaacctttttttctttcaaaatttccaagaaactatgc--ctgtttatgtg---tttttctttattgcagGATGCAACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 7
cgcaacaataatctatataagaaaacctc---actatgtttttctacacaagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
|| ||| | | | || | || ||| | | || || | ||| || | | || | | | | | | || || |||||| ||||| |||||||||||||| |||||||| || || ||||| || ||||| || |||||||| || || ||| |||||||||||||||| ||||| |||||||
ataaaagatagtacacaaaatctattttctaggctaattgtgatagcagtagttttttggtgtaaatgtgaa--tctcagttctacctt-atcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 6
cgcaacaataatctatataagaaaacctcactatg------tttttctacacaagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
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-----caattgatctcacaattcaaatttattgggagtgcatttttctgttaagatcatgtttcttgaatt-ggatttctgaactttgtcttggttgctgatgcagGATGCAACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAAMapped 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|116425639|gb|EG468231.1|EG468231EST: GATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAG GATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGAC
genomic: GATCTGCATTGGCATCAGTTATAATGGGAATGGCTCCAGTCTTGGGTAAGgtaagcagaa ... ttcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
ttcatttc CT-rich tract
attgatattcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgcaacaataatctatataagaaaacctcactatgtttttctacacaagatatttagttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA
- caacaat
- - - - - - - - - - -aaaacct
- - - - - - - - - - - - - - - - - - - - - acacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattttg