Sequence
atgc intronic sequence ATGC exonic sequenceGGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactctagtcacggcgtttcatattttgtatgtgaaaatgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63440.3 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 5'ss of exon 5
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgta------ccaaatcaatccgttattaatcactttttaa------gatttatactctagtcacggcgttt-catattttg---tatgtgaaaatgaggt--tttttgacca-acgcgacacgacctctgtgtttttactctttcag------------
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GAGTGAATGCTGATGATGTTCGAGTAACAGTTGCTGCTCCTGCTGCTCGAGGGGAAGCAAACAACGAACTACTAGAGTTCATGGGCAAGgtgattttctcttatggtacctttattgggaacatgttatcttattgaattccactttcgt-aggatgttcatctactttgagacatgtaaaaatgtgttaatgtttcacaataagcattctgaccctctgatgcgaacaagttcatgctatgaatcag
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv17s0000g01530.t01 (Vitis vinifera), 5'ss of exon 5
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactctagtcacggcgtttcatattttgtatgtgaaaa-tgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
|||| ||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || ||| ||||||||||||| | ||| | | || || | ||| ||| | ||| | || | | | | ||| | | | | | | | | || || |
GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagca------tacttctcattttat---gttttttgtcaaattatcactttttaggtgtcaagcctaactactcaagtcttgcatttggcatag----------------------------
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S121_20V6.1 (Physcomitrella patens), 5'ss of exon 5
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatca-atccgttattaatcactttttaagatttatactctagtcacggcgtttcatattttgtatgtgaaaatga-ggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
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GTGTGAATGCGGATGATGTCCGGGTAACTGTGGCTGCACCTGCAGCCCGTGGTGAAGCAAACAACGAGCTGCTTGAGTACATGGGGAAGgtagcgtctcacatactttcattgaatttcattagaattcgtaa---ggtggtggtgttgtataacacatttgaataattgatggatactttactcctttgtt---------------------------
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S3_299V6.1 (Physcomitrella patens), 5'ss of exon 5
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactcta-----gtcacggcgtttcatattttgt-atgtgaaaatgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
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GTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttcactta--cacttatctccttt-gcgttttgtgaactgatggtgttgggaagattcgtaacaggtcacgtgccaatcaactatttagatatttg-------------------------------
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S3_299V6.2 (Physcomitrella patens), 5'ss of exon 5
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactcta-----gtcacggcgtttcatattttgt-atgtgaaaatgaggttttttgaccaacg--cgacacgacctc-tgtgtttttactctttcag-----------------------------------------------------------
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GTGTGAACGCTGATGATGTCCGTGTAACTGTGGCCGCACCAGCAGCACGTGGTGAAGCAAACAACGAGCTTCTAGAGTACATGGGAAAGgtgtcgcttcactta--cacttatctccttt-gcgttttgtgaactgatggtgttgggaagattcgtaacaggtcacgtgccaatcaactatttagatatttgatttacactccttcgcatgcttcaaatgaggtaggtctattagctggacggagacccaacaatttgaagaacattatgcatatatgtttctag
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ36938 (Selaginella moellendorffii), 5'ss of exon 5
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactctagtcacggcgtttcatattttgtatgtgaaaatgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
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GAGTTAATGCTGATGATGTTCGTGTGACTGTTGCTGCTCCAGCCGCGAGAGGAGAGGCAAACAACGAACTTCTGGAGTACATGGCAAAGgta--aatcaaaccaaaaaacattcgctcgctattaagccaactt--gtaacag--------------------------------------------------------------------------
upper sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ33913 (Selaginella moellendorffii), 5'ss of exon 5
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactctagtcacggcgtttcatattttgtatgtgaaaatgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
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GAGTTAATGCTGATGATGTTCGTGTGACTGTTGCTGCTCCAGCCGCGAGAGGAGAGGCCAACAACGAACTTCTGGAGTACATGGCAAAGgta--aatcaaaccaaaaaacattcgctcgctattaagccaactt--gtaacag--------------------------------------------------------------------------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|19878734|gb|AU239565.1|AU239565EST: CAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGG GTTCTTGGTTTAAGGTTGAGCCAGATGACTCTCCA
genomic: CAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatc ... actctttcagGTTCTTGGTTTAAGGTTGAGCCAGATGACTCTCCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactctagtcacggcgtttcatattttgtatgtgaaaatgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag
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