Sequence
atgc intronic sequence ATGC exonic sequenceCCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50320.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 5'ss of exon 4
CCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtctttataaatatttttagttttctcat-gttagtatcaagtttatcttggcagctt-tcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
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TCAGAGCACATACGAGGATGTTGCACGTGACACAAACAGAGGTCACACTGTAGCTGCTGTTGCTGATTGCTTTTGTTTGGCTAAAGATGCTGGTTTTAAGgtagtctcct-taaatca---ttaatcatctcgtttagtcaacttgttgctggcagca--tttgttaaaataaagtatcatctcatatggttgaactgtttta-atcct-----ccattgattaccttttgatag-----------------------------------------------------
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G100872_T01 (Zea mays), 5'ss of exon 4
CCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtctttataaatatttttagtt-ttctcat-gttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
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CCAGAGTACATATGAAGATGTTGCCCGTGACACAAACAGAGGACACACGGTGGCTGCTGTTGCTGATTGCTTCTGTTTGGCAAAAGATGCTGGGTTTAAGgttattgtttttt--ttagtcac-ataactttgtctgattgctttcattgtttgt-ttatgattattctagttgttttgattcacccttttgacag--------------------------------------------------------------------------------------------
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G359735_T03 (Zea mays), 5'ss of exon 4
CCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtctt-tataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
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CCAGAGTACATATGAGGATGTTGCCCGTGACACAAACAGAGGACACACAGTGGCTGCTGTTGCTGATTGCTTCTGTTTGGCAAAAGATGCTGGGTTTAAGgtttttttttgtcacctagctttgcttaattgattttattatttgtttatgattgttctgactatcttga-----ttcacccttttgacag------------------------------------------------------------------------------------------------
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G18150.1 (Glycine max), 5'ss of exon 4
CCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttgg-cagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
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CCAAAGCACCTATGAAGATGTTGCTCGAGACACAAATAGAGGACACACTGTTGCTGCTGTAGCTGATTGTTTTTGCCTGGCTAAAGATGCTGGTTTCAAGgttttttactct----taatctcaatctgcacactcagtag----aaaacag----aactttgtcctgatcaaccatta--tcctatgtgtccctcctgctgcattttttggat-------------------------------------------------------------------------
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G36790.1 (Glycine max), 5'ss of exon 4
CCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
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CCAAAGCACCTATGAGGACGTTGCTCGAGACACAAATAGAGGACACACTGTTGCTGCTGTAGCGGATTGTTTTTGCCTGGCTAAAGATGCTGGTTTCAAGgttttttact-----cttatctcaatctgcacactcagta-------gaaaacataactttttcctgaccaaccattatcctgtgtgtccctcatgctgcatctttttagat--------------------------------------------------------------------------
upper sequence: AT5G50320.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv17s0000g10190.t01 (Vitis vinifera), 5'ss of exon 4
CCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtct-ttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcc-tatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
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TCAAAGCACCTACGAGGATGTTGCCCGTGACACTAATAGAGGACATACAGTAGCTGCTGTGGCTGATTGTTTTTGCTTGGCCAAGGATGCTGGTTTCAAGgt-------tagatgctaatccattatgaaaatac--acttgccttttgttggaactc--ttgatttgaacttctttcagcaccatttggtttttgcaactagttttctca-----------------------------------------------------------------------------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|125232764|gb|EL246849.1|EL246849EST: CTGGTTTCAAG GTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGAC
genomic: CTGGTTTCAAGgtattccctt ... ttgcctatagGTGGTTGCACATATGATGCCTGATCTTCCTAATGTTGGGGTTGAGAGAGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCAGAGCACATATGAAGATGTTGCCCGTGACACAAATAGAGGTCATACTGTTGCTGCTGTAGCTGACTGCTTCTGCTTGGCTAAAGATGCTGGTTTCAAGgtattcccttatagattagtctttataaatatttttagttttctcatgttagtatcaagtttatcttggcagctttcacctcctatgtttctgttcattaatatccttgaaaccaatgaacatttctttattttagagacactgctaaatttgtatccttacctccgtttttcattttgcctatag
- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG