Sequence
atgc intronic sequence ATGC exonic sequenceGGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggctaccttacacttaaaagtcaaaaatttattgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53900.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os11g25920.1 (Oryza sativa), 5'ss of exon 4
GGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgttttcaatctta-aattttattttttggttagatgtagaaatttatgatcctgatggctaccttacacttaaaagtcaaaaat-ttattgcag-----------
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GGGAAAGGTGGCGTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCGCCAACTACTGGCAGAGCTCTTTTGATGCCgtatgtaccatctcctgcactctcctcctttctctttctgcagag---------ccccctggcccccttgcttttggggggaagagaccttattactgctactactaca
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G302293_T01 (Zea mays), 5'ss of exon 4
GGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgt--tttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggctaccttacacttaaaagtcaaaaattt-attgcag-
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GGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCCTTCGACGCAgtacgtactatcagcagcagctgtgcctctgcacccgcttctttctctttctgcactctgtaacgtacacgtactccatccccacctgttccaaaacaaa
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G132251_T01 (Zea mays), 5'ss of exon 4
GGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggc-taccttacacttaaaagtcaaaaatttattgcag----
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GGGAAAGGTGGCCTCTGATAAATGTCACAAATGGGTCTTCAAGGAACCTTCTGAATGCGAGCCCAACATCTCCAACTACTGGCAGAGCTCTTTCGACGCAgtacgtaacgtacccccatgcatcttcgtcgtcatcat-cagctgtgccccctctgcactgcatctttctctttctgcagtctctctgccacccctgctgc
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G34980.1 (Glycine max), 5'ss of exon 4
GGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgttttca-atcttaaattttattttttggttagatgtagaaatttatgatcctgatggctacct-tacacttaaaagtcaaaaatttat-tgcag--
||| |||||||| |||||||| || ||||||||||| || ||||| || | |||| |||||||||| | | || |||||||| || || |||||||||||| | | || || | || | | | | | | || || | || | | | | | ||| || | |||| || | |
GGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTTGATGCTgtatgagtgcatattctcaactctctccctcc-ccatccaatcacccttctgcttctcttccttttttgtttatttataatatataaatctaaatattgat
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA12G35490.2 (Glycine max), 5'ss of exon 3
GGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgttttca-atcttaaattttattttttggttagatgtagaaatttatgatcctgatggctacct-tacacttaaaagtcaaaaatttat-tgcag--
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GGGGAAAGTTGCATCTGATAAGTGCCACAAGTGGGTCTTTAAAGAGCCCACAGAATGTGAACCAAATATCTCCAACTACTGGCAGAGCTCCTTTGATGCTgtatgtgtgcatattctcaactctctccctcc-tcatccattcacccttctacttctcttccttttttgtttatttataatatataaatctaaatatagat
upper sequence: AT5G53900.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv19s0014g02320.t01 (Vitis vinifera), 5'ss of exon 4
GGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgt-------tttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggctaccttacacttaaa-agtcaaaaatttattgcag--------------------------------------------------------------------------------------------
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GGGGAAGGTTGCATCTGATAAGTGTCATAAATGGGTTTTCAAAGAGCCTTCAGAGTGTGAACCAAATGTCTCCAACTACTGGCAGAGTTCTTTTGATGCTgtaagtaggagaacctcaaacacaaacgttctcttttgattgggtat-----ttgataaaactaattaccattgtgtgggcaaatagtgggtgatttgataaatttggagaaatgggttctttttggcatcatgtcgtggtctattatatgttaatgattgatgatgttcttagcttttggttgaattaattgcagMapped 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|124881202|gb|EH960104.1|EH960104EST: TTACTGGCAAAGTTCTTTTGATGCT CTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
genomic: TTACTGGCAAAGTTCTTTTGATGCTgtacgttttc ... tttattgcagCTTCCTCCAGAATGGACCGACCAATTCGAATCAGGCATTCAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGTAAAGTTGCTTCTGATAAATGTCACAAGTGGGTTTTCAAAGAACCATCTGAATCTGAACCAAATCTTGCTAATTACTGGCAAAGTTCTTTTGATGCTgtacgttttcaatcttaaattttattttttggttagatgtagaaatttatgatcctgatggctaccttacacttaaaagtcaaaaatttattgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG