Sequence
atgc intronic sequence ATGC exonic sequence...ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40670.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G07110.1 (Glycine max), 3'ss of exon 2
ttgttcctttctaagtttcagcaaaaaaaaaacgcttta--gattgttcgagctggtttaatttttt----ttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
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-----attttacaaagctcatccaaacacacactaagtaatgtctgttcttatttatataaatatttggagttccctaatgtagttttagtt-tcatttgtttcagATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTACTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAA
upper sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G23610.1 (Glycine max), 3'ss of exon 2
-ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
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atcactctttttcttttccttgttgaataactatatgatgatatatctgcataaattca-ttagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT
upper sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0219g00130.t01 (Vitis vinifera), 3'ss of exon 2
ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
|| | | |||| | || || || | | || ||| ||||| | || | ||| || ||| || |||||||||||||||||||||||||||||||| ||||| || ||||| ||||| ||| ||| |||| |||||| || ||||||||
-------gtttttattttcgg----------gtctttcaggttttccctcctctttttggatttttaatatg----tggtgaaatgttttcttgttgcagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTGTCTTGATAGCATTTACTTGGTTCCAAATTGCAATCTATGAG
upper sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
-----ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
||| | | | || | | | || || |||| | |||| | | ||| ||||||| | | | || ||| | | ||||| |||||||||||||||||||||||||||||||| ||||| || ||||| ||| | ||||||| |||| |||| || || ||||||||
ttactttgcttatgttaaaagggtggaagagaacaagttgtttaagt-gttccattt--tttcctttttttacaaatatgtggtgata--cgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAGMapped 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|152035112|gb|BP844984.2|BP844984EST: TTAGTCCTGTTATTCAAAAGCAGTACTTTGACACTTATGGCGATAAAGAG ATGATAC-TGTGGCCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGT
genomic: TTAGTCCTGTTATTCAAAAGCAGTACTTTGACACTTATGGCGATAAAGAGgtttgtttcc ... cttatttcagATGATACCTGTGGC-TGCAAATGATGTTGCATTCTCGATCCATGCAGTTGT
EST:
gi|125248666|gb|EL262751.1|EL262751EST: ACACTTATGGCGATAAAGAG ATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGAT
genomic: ACACTTATGGCGATAAAGAGgtttgtttcc ... cttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
gtttaat putative branch site (score: 4)
cttatttc putative PPT
tttaattttttttgag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - -cctttct
- - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - aaaacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttttgt