Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G55280.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 4
------------------------------------------------------------------------------------------------------------gtaatgtgtgttgacaccgtttc-----ttgttgaatgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
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gtgtgctaaaaaacttggaatttcctttttttcatttatactcatttgcagctagtcataaatcatgtgttattaacttataataatcttagttatggatgaactatgatcatgtattttgataattttttgatgtttattatattgtcttgcttcgaggatactttgagaggttaaattcagatgtcatcctttc----agGCACTGGAAGCCATTGAAAAGCTGCAGAAAAATGTGGATACACTTATAGTGATTCCAAATGACCGCCTGCTTGACATGGCTGATGAGCAGACACCTCTTC
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 4
gtaatgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
||| | || | | || || || | || | | | | | | | | ||| || ||| | || ||||| ||||||| ||||||||||| || || ||||| ||||| ||||| |||||||||||||| || ||||| || || |||||||| ||||| || ||||
gtattttgaaaattggttgatgtttattatattgtcttgctctgaggatacttggagaggttaaattaagat---gtcatt-cttccagGCATTGGAAGCCATTGAAAAGCTGCAGAAAAATGTGGATACACTTATAGTGATTCCAAATGACCGCCTGCTTGACATGGCTGATGAGCAGACACCTCTTC
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 3
----------gtaatgtgtgttgacaccgtttcttgttgaatgggtttaagttt-aaagtcttgtta-tggatctatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
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ttttatctagctgataagagtctatggttcatctgaaacttttagtttgtgttttgaaatctagaaaataagtctctagtttgcatt-tggttttcttcagGCCTTTGAAGCCATCGAAAGGCTGCAGAAAAATGTTGACACACTTATAGTGATTCCAAATGACCGTCTGCTTGACATAGCTGATGAGCAGATGCCTCTTC
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 3
------gtaatgtgtgtt-gacaccgtttcttgttgaa----tgggtttaagtttaaagtcttgtta-tggatctatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
||| | | | | ||| | | || | | || |||| || ||| | | | ||| | | | | ||| || |||| | ||||| || |||| ||| || || |||||||| || ||||| || |||||||||||||||||||| || || |||||||| |||| ||| ||||
ttttatgtagcagataagagtctgtggttcatctgaaacttgtagtttgtcgtttgaaatctagaaaataagtctctagtttgcatt-tggttttcttcagGCCTTTGAAGCCATCGAAAGGCTGCAGAAAAATGTTGACACACTTATAGTTATTCCAAATGATCGTCTGCTTGACATAGCTGATGAGCAGATGCCTCTTC
upper sequence: AT5G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 3
----------gtaatgtgtgt-tgacaccgtttct-tgttgaatgggtttaagtttaaagtcttgttatggatc-tatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
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ctaattccaagtttcaagcttatgattttgcagctgtatcaaatatgttgtactatattgagttccaaacagtcatgtgttgtatttgct--tttgttttagGCATTGGAGGCTATTGAAAAGTTGCAAAAGAATGTTGACACACTAATAGTAATTCCCAATGATCGTCTGCTGGATATTGCCGATGAACAGACACCTCTTCMapped 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|301501112|gb|HO206652.1|HO206652EST: GTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAG GCACTGGAAGCTAT
genomic: GTGTTGTTACCTATCCGTTTAGCTTTGAAGGACGTAAAAGATCTTTGCAGgtaatgtgtg ... tttcctctagGCACTGGAAGCTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
gcctgat putative branch site (score: 4)
ttatttcctct putative PPT
agtttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtgtgttgacaccgtttcttgttgaatgggtttaagtttaaagtcttgttatggatctatgcctgatttggttatttcctctagGCACTGGAAGCTATTGAAAAGCTCCAAAAGAATGTTGATACCCTTATCGTGATTCCAAATGATCGTCTGCTAGATATTGCTGATGAACAGACGCCACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT