Sequence
atgc intronic sequence ATGC exonic sequenceAAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03540.3 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G074530_T01 (Zea mays), 5'ss of exon 1
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag
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AAGAAGCTGTTGAAAAGGATGCAACAAAGAATATTCATACTGATGGAACAGTTCATCCTTTAACAAGCTATGTGATCAACTATGTTAAGTTTTTGTTTGAgtaagta------------tctaatcaaatccgcatgcaatttatgtgttgttataaatga-ataggtgtacaagatttgtccttatccatgtgcctttccttttctaattat-----
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 7
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag
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AAGAGGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACAGATGGAACTGTCCATCCTCTAACAAGCTATGTAATTAACTATGTGAAGTTTTTATTTGAgtaagttcagc-tatgttgtcatctgat--cccaattttgtagccgcatcaattatttc--tagcattttttgc----tgtgttcactgatgacaaaaatgttagtcat---------
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 7
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag-
|||| || ||||||||||||||||| |||||||| || ||||||||||||||| || |||||||||||||| || || ||||| ||||||||||| |||||||| || | ||| | ||| || || | | || ||| |||||| | || | | | ||| | || | |||||| || ||| ||
AAGAGGCAGTTGAGAAAGATGCTACGAAGACTGCAGTAACAGATGGAACTGTCCATCCTCTAACAAGCTATGTAATTAACTATGTGAAGTTTTTATTTGAgtaagttcagc-tatgttgtcatctgatccc--------aattttgtag---------ccataccatcaattatttctagcattttttgctgtgttcactgatga-caaaaatgttagt
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 7
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactattt-gcgtattgttcttctccatactgctat-ttgcgtattgtccctttccacgctttaattgatgatcat-tggtgtcag
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AAGAAGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACTGATGGAACTGTCCATCCTTTGACAAGCTATGTGATTAACTATGTGAAGTTTTTATTTGAgtaagt---tcatttctgctgtattc--tgcttcaaattctcgagcgcact---------catgaagttatgtctagcattgtatatt-----gttttaattggtgagaaagctgcgtc--
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA20G17500.1 (Glycine max), 5'ss of exon 4
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgc-gtattgtccctttccacgctttaattgatgatcat-tggtgtcag
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AAGAAGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACTGATGGAACTGTCCATCCTTTGACAAGCTATGTGATTAACTATGTGAAGTTTTTATTTGAgtaagt---tcatatgtgctgtattc--tgcttcaaattctcaac--------cacacccatgaagttatctctagcattgtatatt-----gttttcattggtgaaaaagctgcatc--
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag---
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AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctc----tgactgtgttgctatcttctagctcc------attcttttgggcaagacagata-------acagtttcat-ccatgc--taattggtggt-atttctattagggt
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: PP1S39_74V6.1 (Physcomitrella patens), 5'ss of exon 7
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag
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AAGATGCTGTGTCAACAGATGCGACAAAGACGCCTGTTTTGGATGGAACAGTCCATCCCCTCACAAGCTATGTCATTAATTATGTCAAATTTCTTTTTGAgtaagagctctctctct-ctcggtatatacacacaca-tatacactcacaa-----acacacacttttagttagttggtttatttgtcttc-ttttatttggttttta----------
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EFJ18152 (Selaginella moellendorffii), 5'ss of exon 7
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag
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TGGATGCTGTGGAGAAAGACGCAACAAAAACTGCTGTCCAGGATGGTACGGTCCACCCGCTTACGAGTTACGTCATTAACTATGTCAAGTTTCTCTTTGAgtaagtggttaatctg----cctctggtagctggacataacttgctgtttgtttgtctcc-tgtggtttcgagcag------------------------------------------Mapped 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|125005340|gb|EL077609.1|EL077609EST: GTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGA CTACCAAACAACATTGAAGCAAC
genomic: GTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacat ... ttggtgtcagCTACCAAACAACATTGAAGCAAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AAGAAGCTGTTGAGAAAGATGCTACAAAGACTGCTGTTCTAGATGGAACTGTCCACCCACTAACAAGCTATGTCATCAATTATGTCAAGTTTTTATTCGAgtaagtacatcatatatactcaacttatttcctcgaactatttgcgtattgttcttctccatactgctatttgcgtattgtccctttccacgctttaattgatgatcattggtgtcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT