Sequence
atgc intronic sequence ATGC exonic sequenceTTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagtactgaagctagcatgtgccgaatcttttgaatcagaattgtggtctcttactttgggatattgagcag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19170.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os06g48650.2 (Oryza sativa), 5'ss of exon 8
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattg--atagtactgaagc---tagcatgtgccgaatcttttgaatcaga-attgtggtctc----ttactttgggatattgagcag-----------------------------------------------------------------------------------
||||||||||||||| |||| || || ||||| || || || || |||| |||||||| || ||| || |||||||| |||||| ||||||||| |||||||| ||| || | | | | | | | | |||| | | || || | | || | | || || |
TTTCAAGATGCTGATGTTCTAAAGCCTGATATACTCGCTCCTGGCAATCTTATATGGGCAGCATGGGCGCCTAATGGAACTGATGAAGCCAATTATGCTGgtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttgattgttctatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccag
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G099452_T02 (Zea mays), 5'ss of exon 9
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagta------------ctgaagctagcatgtgc-cga--atcttttgaatcagaattgtggtctcttac-----tttgggatattgagcag----------------------------------------------------------------------
||||||||||||||| | |||||||| || || ||||| || || |||||||||||||||| ||| || ||||||||||||||| | ||||||| |||||||| ||| ||| || ||| |||| || ||| | || | || || || || | ||| | ||||| | |
TTTCAAGATGCTGATGTCCTTAAACCAGACATACTTGCTCCTGGCAATCTCATATGGGCTGCATGGGCGCCTAATGGAACAGATGAATCAAATTATGCTGgtaagctttgtatgtagatctctttttcctcaaggaagcacccatgtgattatcgccagcattttagttctgcgcttttgccgtccttttgcatattttgtggactagtgattcttgaggatatctttctgtgcttgaaccaattcaaaattgttgtggtaatattttcgcag
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G114394_T02 (Zea mays), 5'ss of exon 9
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagtactgaagctagcatgtgccga----------atcttttgaatcagaattgtggtctcttactttgg--gatattgagcag------------------------------------------------------------------------------
||||||||||||||| | |||||||| || || ||||| || || |||||||||||||||| ||| || |||||||| |||||| | || |||| |||||||| | | || | | ||| || || ||||| ||| | | || | | | ||| |||
TTTCAAGATGCTGATGTCCTTAAACCAGACATACTTGCTCCTGGCAATCTCATATGGGCTGCATGGGCGCCTAATGGAACGGATGAATCAAACTATGCTGgtaagcgtgcgttgtctgtagacctcttcccctcgaggaagcacccatgattaccatcagtattttactactgcgctcttgccgcccttgtgcatatcttctggattagtgatcggtggtgatatttttctgtgctcgaaccaactcaacattgctgtggtaatatttctcag
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G06740.1 (Glycine max), 5'ss of exon 8
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagtactgaagc--------tagcatgtgccgaatcttttgaatcagaattgtggtctcttactttgggatattgagcag---------
|| ||||| || |||||||| ||||| ||||| | || || |||| | || |||||||||||||||||||||||||| ||||| || ||||||||||||||| | || ||| || | | ||| || | | |||| | | || | || | |
TTCCAAGAGGCAGATCTTCTCAAACCAGATATATTAGCTCCTGGTTCATTGATTTGGGCTGCTTGGTGTCCAAATGGAACTGATGAGCCAAATTATGTTGgtaagtaatggcttgactaaattgtcttctttgttgttacttgaaaacttctacctacaattatacatttcaacctcatgacctgggcttaagctcatat
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA13G00580.1 (Glycine max), 5'ss of exon 8
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagtactgaa--gctagcatgtg--------ccgaatcttttgaatcagaattgtggtctcttactttg-----ggatattgagcag--
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TTCCAAGAGGCAGATCTTCTCAAACCAGATATATTAGCTCCTGGTTCATTGATTTGGGCTGCTTGGTGTCCAAATGGAACTGATGAGCCAAATTATGTTGgtaagtaatggcttgactaaattgtctttttgtggttgttacctgaaaacttttacctacaattatgcatttcaaccttattaccagggcttaagctcat
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA15G17830.1 (Glycine max), 5'ss of exon 8
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagtactgaagctagcatgtgccgaatcttt--tgaatcagaattgtggtctcttactttgggatattgagcag----------------------
|| ||||| || |||||||| ||||| ||||| | || || |||| | || ||||||||||||| || ||||||||| ||||| || ||||||||||||||| | || | ||| | | || | | ||| || || | | |||| | || |||| || | | ||
TTCCAAGAGGCAGATCTTCTCAAACCAGATATATTAGCTCCTGGTTCATTGATTTGGGCTGCTTGGTCTCTAAATGGAACCGATGAGCCAAATTATGTTGgtaagtaatggtttgactaa--tttgcct---cttaattgttgatgtttgaaaatttctgcctactact--aaagtactaaacaattacctcactactgtgcttagc
upper sequence: AT2G19170.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 5'ss of exon 9
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagtactga---agctagcatgtgccgaatcttttga-atcagaattgtggtctcttactttg--ggatattgag-cag----------
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TTCCAAGATGCGGATCTTCTCAAACCAGATATTCTAGCTCCAGGTTCTCTCATTTGGGCTGCCTGGTCTCCAAATGGAACAGATGAGGCCAATTATGTTGgtaaatatcagtagtttcaattcatctatttctccctacttctttagatgtcttagccaaggcttaatctttatatgcgcattaagtcagtcaatccagaMapped 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|47829262|gb|CK118946.1|CK118946EST: ATGAACCCAATTATGTTG GTGAAGGATTTGCGCTAATATCAGGAACCAGCATGGCTGCACCACACATAG
genomic: ATGAACCCAATTATGTTGgtaagcattg ... tattgagcagGTGAAGGATTTGCGCTAATATCAGGAACCAGCATGGCTGCACCACACATAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTCAAGATGCTGATCTTCTTAAACCGGATATTCTTGCACCCGGTTATCTCATATGGGCTGCTTGGTGTCCAAATGGAACAGATGAACCCAATTATGTTGgtaagcattgatagtactgaagctagcatgtgccgaatcttttgaatcagaattgtggtctcttactttgggatattgagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG