Sequence
atgc intronic sequence ATGC exonic sequencegtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G01690.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 3'ss of exon 3
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagat--tttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
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---------------------------------------------------gtgtttattgtagtgt-gcaattgctgttttgtttttgatgattcagataagaatacggtgatttcggtgcttagGTGTGTATGCTGGTGATCCTTCAAAGCTCAGTATGAAGGCTGCATTTGGGAAGGTGTGGAGGCTGGAGGATACTGGAGGTAGCATTATTGGTGGAACCAT
upper sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G039396_T01 (Zea mays), 3'ss of exon 3
gtagagttatagataaaacttcatgtgaaccatttatt-catttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
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-----------------------------gtgcttattgcagtgtgttattgttgtttgttctggcctgctacttgcagcggttagccgattaccataagaatttaacaactttgtaaacctaagGTGTCTATGCTGGTGATCCTTCTAAGCTCAGCATGAAGGCTGCATTTGGGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCAT
upper sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 5
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT--
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---------------------ca-atgtcccattttctctcctattatgaattttcttctgtttttcagcagtttt---ttttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAA-AAAATGGTGGTAGCATAATTGGTGGAACTTTCA
upper sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G27890.1 (Glycine max), 3'ss of exon 3
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
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----------------tacttcatctagcttttctctcctattatgaattttc---ttctgtttttcagcagtcttttttattg----aaaattctgttgcttacctgaattttgt-tatatagGGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTCGGGAAAGTTTGGAAGCTGGAAAAAAATGGTGGTAGCATTATTGGTGGAACTTT
upper sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 3
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
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---------ctgtcaaaagttt-tatgaa------gttca--cagaattcaccgactcttgtcattttaga----tggttgttgctcaggccga--tttcattggaaatgttttttgtatgcagGTGTTTATGCAGGAGATCCTTCAAAACTGAGCATGAAAGCAGCATTTGGAAAAGTTTGGAAGCTTGAGCAGAAGGGTGGTAGTATAATTGGTGGCACCTT
upper sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ23527 (Selaginella moellendorffii), 3'ss of exon 3
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
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-----------------------------------------------------------------------gtgagtactatttgattggcgtagatttt-ccccttagttg----gatttcagGCGTTTATGCTGGTGATCCTTCGAAATTGAGTATGAAAGCTGCATTCGGGAAAGTATGGAAGCTGGAAGATCAAGGTGGAAGCATCATCGGGGGAACTAT
upper sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ34803 (Selaginella moellendorffii), 3'ss of exon 2
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
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-----------------------------------------------------------------------gtgagtactatttgattgacgtagattt--tcctcttagttggat---ttcagGCGTTTATGCTGGTGATCCTTCGAAATTGAGTATGAAAGCTGCATTCGGGAAAGTATGGAAGCTGGAAGATCAAGGTGGAAGCATCATCGGGGGAACTATMapped 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|124980297|gb|EL053259.1|EL053259EST: TAACCTCGGTGATGAGGTTTTTGAGCGCCTGATTGAACCGTTTTGTTCAG GTGTTTATGCTGGTAGATCCTTCAAAACTGAGCATGAAAGC
genomic: TAACCTCGGTGATGAGGTTTTTGAGCGCCTGATTGAACCGTTTTGTTCAGgtagagttat ... atgcttttagGTGTTTATGCTGGT-GATCCTTCAAAACTGAGCATGAAAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
ccttaat putative branch site (score: 4)
tgctttt putative PPT
attttatgctttta TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG