Sequence
atgc intronic sequence ATGC exonic sequenceGGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatagcttccaaaagataaatttttttccatgcatccagttgatgttaaccaaccagttgtgctatttttcttttagttcatgatcatgttcgccgtta...
Basic information
species | Arabidopsis thaliana |
transcript | AT4G05420.2 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os05g51480.1 (Oryza sativa), 5'ss of exon 4
GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatagcttccaaaagataaatttttttccatgcatccagttgatgttaaccaaccag--ttgtgctatttttcttttagttcatgatcatgttcgccgtta
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AATGAGACTCAGGACTTCCTTTTCATTGCGACTGAAAGATACAAATTCTGTGTTCTGCAGTGGGATGGAGAAAAATCGGAGCTTCTCACTAGgtttggtcacttgcac-tattctctttagcttacaaagcaatgagactgcttttataaccttttatagacataacattggcttgtcaaatggttcaa-attg
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os05g51480.2 (Oryza sativa), 5'ss of exon 3
---------GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatagcttccaaaagataaatttttttccatgcatccagttgatgttaaccaaccagttgtgctatttttcttttagttcatgatcatgttcgccgtta
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CTATCTATGGAAGAATCGCCACACTAGAGCTCTTCCGCCCTCATGTCA-GCCAATTTACTGTTCCTCGACTTGCCATTCTGTTGTTGCCGTGCACTGGATGgtaaaact-----aacactatttatcttacgcctttcagaatgagactcag-gacttccttttcattgcgactgaaagatacaaattctgtgttctgcag
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G402002_T01 (Zea mays), 5'ss of exon 4
GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatag--cttccaaaa------------gataaatttttttccatgcatccagttgatgttaacc--aaccagttgtgctatttttc-----ttttagttcatgatcatgttcgccgtta------------------------------------------
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AATGAGACTCAGGACTTTCTTTTCATTGCTACGGAGAGGTACAAATTCTGTGTTCTGCAATGGGATGCAGAAAAGTCAGAGCTAATCACCAGgtttggacatgccatgacctttttactttactaagtatggatttatggttccacttaatgttgtccgtaggaaaacatatggtcattcagcgatatatgttgattgaaatgctggcgttccctatttttgtttggaaaataatggtttgtttgtaatatgtag
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G30530.1 (Glycine max), 5'ss of exon 4
GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatagcttccaaaagataaatttttttccatgca-tccagttgatgttaaccaaccagttgtgctatttttct-tttagttcatgatcatgttcgccgtta
|| ||||| || || | | | || ||||||||||| |||||||||||||||||||||||||||||| |||| | |||||||| ||||| ||||| | || || |||| ||| | || | | | || | || | | ||| | ||| | || | ||| || | || |
GGTGAAGCACAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCTGAAACTGCTGAGCTTGTTACACGgtatgtgtgaggaagcatcaattctttcctttggagtggacttacttttgttctgcttgtttttgtatagatagattgaaatcaacattgtttttaattt--
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G13680.1 (Glycine max), 5'ss of exon 4
GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatagcttccaaaagataaatttttttccatgcatccagttgatgttaaccaaccagttgtgctatttttcttttagttcatgatcatgttcgccgtta-
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GGTGAAGCGCAGGATTATCTTTTTATTGCAACTGAAAGATACAAATTCTGTGTTCTTCAATGGGATTCCGAGACTGGTGAGCTTGTTACACGgtatgtgtgaggaagcaccaattctttcctttggagtggatttacttgtgtccagta-ttgtttttgtatagattgaaatcaacattgtttttaatcataa
upper sequence: AT4G05420.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv10s0003g04360.t01 (Vitis vinifera), 5'ss of exon 4
GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtata-gcttccaaaagataaatttttttccat-gcatccagttgatgttaaccaaccagttgtgctatttttcttttagttcatg--atcatgttcgccgtta
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GGCGAAGCACAAGATTTTCTATTCATCGCAACTGAAAGATACAAGTTTTGTGTTCTTCAATGGGATGCAGAGAATTCTGAGGTTATTACAAGgtttaagcatgaaacagaaacaacatttactttagtgttcatttcatttatgatgttccgtt-tgctagtttaccactattttaagttattacattttcta---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|116483004|gb|EG525596.1|EG525596EST: AAATTCTGTGTTCTTCAATGGGATCCTGAGCCCTCTGAGCTTATTACAAG AGCAATGGGGGATGTTTCTGATCGTATAGGCCGGCCAACAGACAATGGTCA
genomic: AAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatagcttc ... cttttttcagAGCAATGGGGGATGTTTCTGATCGTATAGGCCGGCCAACAGACAATGGTCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCGAAGCGCAAGACTTTTTGTTCATTGCAACTGAGAGATACAAATTCTGTGTTCTTCAATGGGATCCTGAGTCCTCTGAGCTTATTACAAGgtatagcttccaaaagataaatttttttccatgcatccagttgatgttaaccaaccagttgtgctatttttcttttagttcatgatcatgttcgccgtta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaagat