Sequence
atgc intronic sequence ATGC exonic sequenceAGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat...
Basic information
species | Arabidopsis thaliana |
transcript | AT2G40470.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g60960.1 (Oryza sativa), 5'ss of exon 2
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat
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GGAGTGCCCCTTCGCCCCCTACTTCTCGCCGCACGAGCCCCACAAGTTCGCCGCCGTCCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgta----cgataccattacaggtcaaagcattccttaaattgtacctttcgcta--gcttgtgcattaatggcttcgtcggtgcaatgcggtt-tcag--
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g07270.1 (Oryza sativa), 5'ss of exon 1
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgt-aatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaac-aataaccaactgatggtaatctagtggtcatat--
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GGAGTGCCCCTTCTCGCCGTACTTCTCGCCGCTGGAGCCGCACAAGTTCGCCTCCGTGCACAAGGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCCTGgtgagtagtgatc---gagctgggttaagcttaat-taagcatatgcatccatccatggtgacctagctagcaagaggcttatattaattaattggttgaactc
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G092517_T01 (Zea mays), 5'ss of exon 2
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat
||||| ||||| | || || ||||| || || ||||| || || ||||| |||||||||| ||||| || ||||| ||||||||||||||||| |||||| |||| |||| | ||| | || || ||| | || ||| | | | || | | || | |||| |
GGAATGCCCCTTCGCCCCTTACTTCTCGCCGCATGAGCCCCACAAATTCGCCGCCGTCCACAAGGTCTTCGGCGCTAGCAACGTCTCCAAGATGCTCTTGgtaa-agcc---tcaa----cttgaagaaaaaatcgtgcttttctagtctatagttaaa-agatttcagtgtagacttgtaaacgtgtcgattgtcacag
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA06G15050.1 (Glycine max), 5'ss of exon 1
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaa-tagccat-ttcaaaacacacatagat---atggtcttgatttatgcatgcattattacat-atgtaaca-ataaccaactgatggtaatctagtggtcatat-----------------------------
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AGAATGTCCCTTTTCTCCATATTTCTCTCCCCATGAGCCTCAAAAGTTTGCTTCTGTCCACAAAGTCTTTGGTGCCAGCAACGTCTCAAAGATGCTCATGgtaaatatacacacacacggtacacataaataacactagctagctagttatttaattaaccatatcatataacatgtattccacttattatagattt-taatcatatcatataatttcttcgacaatgtgttgtag
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA04G39830.1 (Glycine max), 5'ss of exon 1
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaa-tagccattt---caaaacacacatagata----tggtc--ttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat-------
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AGAATGTCCCTTTTCTCCATATTTCTCTCCCCATGAGCCCCAAAAATTTGCTTCTGTCCACAAAGTTTTTGGTGCCAGCAACGTCTCAAAGATGCTCATGgtaaatacacacacacacactgtacacataaataacactggctagctagttatctaattaatcatatcatatacatgtgtattccacttattatagattt-caatcatatgttgtag
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv13s0067g02380.t01 (Vitis vinifera), 5'ss of exon 2
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagcc-atttcaaaacacacataga----tatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat
|||||| |||||||| || || ||||| || || || || || ||||| |||||||| ||||||||||| || || || ||||||||||||||||| |||||| | || | ||| || ||| ||| |||||||| || || || | || || | ||| | || | |
AGAATGCCCCTTTTCTCCCTACTTCTCTCCCCATGAACCCCAGAAGTTTGCTTCCGTTCACAAAGTCTTCGGCGCCAGCAACGTCTCCAAGATGCTCATGgtagaaccctaattctgtctaccagtagtatttcatgttcttgattgattgataacttct--caaatcttacactgttaaattcag-------------------
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ35900 (Selaginella moellendorffii), 5'ss of exon 1
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataacca--actgatggtaatctagtggtcatat-
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AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaatcatccctcttctct-tcccgtggcaatccgagcac-cactattccat-tgtctttctaagtggtactcttttctctttcggagtgtgctt
upper sequence: AT2G40470.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ09483 (Selaginella moellendorffii), 5'ss of exon 1
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgta-atagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat--
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AGAGTGTCCCTTTGCACCATACTTCTCGCCACACGAGCCTCAAAAGTTTGCCGCCGTCCACAAAGTTTTCGGCGCCAGCAACGTCTCCAAGATGCTCTCGgtacgtgatcaatcatctctcccctcctctcttcccgtggccc-tccgagcaccactattccattgtcttt--ctaagtggcactcttttctctttcggagtgMapped 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|86082783|gb|DR378542.1|DR378542EST: CCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGYTAATG GAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAA
genomic: CCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagcca ... aactaatcagGAAGTACCTGAGAGCCAGAGAGCAGATGCCGCGAATAGCCTTGTGTATGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AGAATGTCCCTTTTCGCCATATTTCTCCCCACACGAGCCTCATAAGTTCGCTTCCGTCCACAAAGTCTTTGGAGCTAGTAACGTCTCCAAGATGCTAATGgtaatagccatttcaaaacacacatagatatggtcttgatttatgcatgcattattacatatgtaacaataaccaactgatggtaatctagtggtcatat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaataac