Sequence
atgc intronic sequence ATGC exonic sequenceCAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G09210.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os07g14270.3 (Oryza sativa), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatc-tcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag
| || ||||| ||||||||||||||||| |||||||| || | ||| | || |||||||||||||||| |||||||||||||| |||||||| |||||||| || | | || | |||| || ||||| | | |||| | | | | || | | |||| |||||
CTGTAAAGCATGAGCAAAAGCTTGACTGTGGTGGTGGATATGTCAAGTTGCTTGGTGGTGATGTTGACCAGAAGAAATTTGGTGGGGACACACCGTACAGgtaatgattttcttctattgtagctctgat--tctcacttttctcaagattagtactagttatctaacttggta-----------cttttgaatgcag
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g61670.1 (Oryza sativa), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag
| || ||||||||||| ||||| |||||||| || |||||| |||| | || |||| || |||||||| ||||| |||||||| || || || ||||||| | || | ||| | || ||| | | | ||| | | | | | || | ||||| | |||||
CGGTGAAGCACGAGCAGAAGCTCGACTGCGGCGGCGGCTACGTGAAATTGCTCGGTGGCGACGTTGACCAGAAGAAGTTTGGTGGCGAGACGCCGTACAGgtgatggtttaatttgatcacttcgcattcccctctgtgtgctcatttcagagcgcaacatctttgattgat----cagtttcttttgaaattgcag
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G358059_T01 (Zea mays), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGT---GATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag
| ||||||||||| |||||||||||||||||||||||| | ||| | || ||||| ||||| ||||| ||||||||||||||||||||| | |||||||| | | || | | || | || ||||| || | ||| | || |||| | ||| ||| | ||| |||||
---TGAAGCACGAGCAGAAGCTTGACTGCGGTGGTGGCTACGTCAAGTTGCTGGGTGGTGGTGATGTAGACCAGAAGAAATTTGGTGGAGACACATCTTACAGgta--gactttgaacaatattgttgcgctcct-tctccctatcat------atctcatcttgtacttgtaac--ctcatt--cttctgtac-tgcag
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G074687_T01 (Zea mays), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag
| || ||||||||||| ||||||||||| |||||||| ||| | ||| | || |||||||||| ||||| || ||||| ||||| |||||| | |||||||| ||||| || || | || ||||| || | | | | || | || | | | | || | |||||
CTGTGAAGCACGAGCAGAAGCTTGACTGTGGTGGTGGTTACGTCAAGTTGCTGGGTGGTGATGTAGACCAGAAAAAATTCGGTGGGGACACAACTTACAGgtag----cctatggatatattcttgtactttttctccctatcat------atctgatcttgtagtagtagttaac--ttcattcttctgtatgcag
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G23080.2 (Glycine max), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaa-taacaacc---catctgcttttttacctgcag
| |||||||| || || |||||||||||||||||||||||||||||| | || |||||||||||||| || |||||||||||||| || || || ||||||| |||| | | | | | | ||| | || | ||| | | || | | || ||| || | || | |||||
CTGTCAAGCATGAACAGAAGCTTGACTGCGGTGGTGGCTACATGAAGTTGCTCAGTGGTGATGTTGATCAGAAGAAATTTGGTGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgttgctctttcctgatgggtgcctctcat-atcgcaaaacacctgaccttttaacatttgttgttctgt-tgcag
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G28890.1 (Glycine max), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag------
| || |||||||| || ||||||||||| |||||||||||||||||| | || ||||| |||||||| || ||||||||||| || || || || ||||||| |||| | | | | | | ||| | || | | | ||||| |||| | | | | || ||| | | |
CTGTTAAGCACGAACAGAAGCTTGACTGTGGTGGTGGCTACATGAAGTTGCTCAGTGGGGATGTTGATCAGAAGAAATTTGGCGGGGATACTCCTTACAGgtgatttatatatccccttttgatttgctgctctttcctgat----gggtgcctttgatgttgtaaaacagctgatcttttgacatttgttgttctgttgcag
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgt-acaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag
| || |||||||| |||||||| || || |||||||||||||||||| | || |||||||| ||||| ||||||||||||||||| || || || || |||| ||| | | | || || | | ||| | | | || | ||| || | |||| | | | | | ||||||
CTGTTAAGCACGAACAAAAGCTAGATTGTGGTGGTGGCTACATGAAGTTGCTCAGTGGTGAAGTTGATCAAAAGAAATTTGGTGGTGATACCCCTTATAGgtgacatgtgcctctgctgaacaatcctttttgctcctttcaattttctttcctagttgggttctaacctgacaaattttgtattctgtggactgcag
upper sequence: AT1G09210.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 3
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaatt---aacatcaa----tgtttaaaaataacaacccatctgcttttttacctgcag
| || || || || || ||||||||||| |||||||| ||||||||| | || |||||||| ||||| ||||||||||||||||| || || |||||||||| | | ||| | || ||| || | || | | | | ||| || |||||| | | | | |||||
CTGTTAAACATGAACAGAAGCTTGACTGTGGTGGTGGATACATGAAGTTGCTCAGTGGTGAGGTTGATCAAAAGAAATTTGGTGGTGATACCCCATACAGgt--cagtgttatttttgcttactgtttgtttgtccctttgtctatgactccaaacttcttatcccttttaaagttgttgatttgttataaaacatgattgcagMapped 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|164179309|gb|ES173646.1|ES173646EST: AATTTGGTGGAGACACACCATACAG TATCATGTTTGGTCCTGATATCTGTGGCTACAGCACAAAAGAAAGTGCATG
genomic: AATTTGGTGGAGACACACCATACAGgtacaaatcc ... ttacctgcagTATCATGTTTGGTCCTGATATCTGTGGCTACAGCACAAA-GAAAGTGCATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGTCAAGCACGAGCAAAAGCTTGACTGCGGTGGTGGCTACATGAAGCTACTAAGTGGTGATGTTGACCAAAAGAAATTTGGTGGAGACACACCATACAGgtacaaatcctatctcatctcactcttatcatctcaacctattatcaattaacatcaatgtttaaaaataacaacccatctgcttttttacctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA