Sequence
atgc intronic sequence ATGC exonic sequencegtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G13320.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 5
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
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----------------------------------------------------gtattatttgtcctagctgaattcaacctatt-attgcagggaaaccatgtgtctgaa--ttcttgagtatcatgtaaaccca-tagccttttcaaatggattaactgtaaatctc----tgcttttgggattagAG-CTGATTTGGTGCCTGCCTATGTTCGCCTCCTTCGTGATAATGAGGCTGAAGTGCGGATAGCAGCTGCTGGAAAAGTAACTAAGTTTTGCCGCATATTA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 5
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
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---------------------------------------------gtattatttgtgctagctgaattcaacctatt-attgcagggttgtaaaacat---gtatctgaa--tttttgagtatcatgtaaaccca-taaccttttctaatggattaactgtatatc----tatgtttttgggattagAG-CTGATTTGGTGCCTGCATATGTTCGTCTCCTTCGCGATAATGAGGCTGAAGTGCGAATAGCGGCTGCTGGAAAAGTAACTAAGTTCTGCCGCATATTA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 5
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaat-tctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
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---------------------------------------------gtgttcaatcttctttctttatgttaaa-aatgattctttgacat--aaattgattattgctt-------tatacatggaaagattaatcaacataatgccatgactcgtttactattgagac-cat-tgccttttataatagGGGTG-ATCTGGTGTCAGCGTATGTTCGCCTTCTCTGTGACAATGAGGCTGAAGTGCGGATTGCAGCTGCTGGAAAAGTTACAAAATTCTGCAAAATATTA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 5
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattac-tgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
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----------------------------------------------------------------------------aaatcatgtgatttttg---tattgattatct-----cttatgattaccaaggcccaactctgaagcc---taagcaatatatttatttttcttaactattgtttgtgt--agAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGTGATAATGAGGCTGAAGTACGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 5
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
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---------------------------------------------------------------------------taatcatgtgatttttg---tattgattatct-----cttatgattactaaggcccaactctgaagcc---taagcaatatatttatttttcttaacta--ttgtttatgaagAACGGAATTGGTACCTGCTTATGTGCGGTTGCTTCGAGATAATGAGGCTGAAGTGCGCATAGCAGCTGCTGGAAAAGTGACCAAGTTTTGCCGGATTTTA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 5
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgt-attaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
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---------------------------------------------------------------------------------attgatttcc----tcttatatttacgaaggtccagattcagtg--tcctataaatttaactggttatgt--ttcttaagattttctcgtcactattattttgtaaagAACGGAATTGGTTCCTGCCTATGTGCGGTTGCTTCGAGACAATGAAGCTGAAGTACGGATTGCAGCTGCTGGGAAAGTGACCAAGTTTTGCCGGATATTA
upper sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttgg--tacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
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-----------------------------------------------------------------------------------taatctcaagttttcctggcttatcttgatttcctttctttctttctt-tctttctttttttttttttttttttttttgtggtgactgatat------cattttaagAACGGACTTGGTTCCCGCTTATATGCGGTTACTTCGAGATAATGAGGCTGAAGTACGAATAGCAGCTGCTGGCAAAGTAACTAAATTCTGTCAGATCTTAMapped 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|116425639|gb|EG468231.1|EG468231EST: AGGACCGGAGCCAACTAG GACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGA
genomic: AGGACCGGAGCCAACTAGgtaagcagtg ... atgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGA
EST:
gi|125296846|gb|EL310931.1|EL310931EST: TTTGTGAAGCTGTAGGACCGGAGCCAACTAG GACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGA
genomic: TTTGTGAAGCTGTAGGACCGGAGCCAACTAGgtaagcagtg ... atgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
tcttaat putative branch site (score: 3)
ttttttatactttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcagtgatggttgaagttagttatggtttaatgtagtattgacctttagtatgcaattctatatcaaacaatagattactgacttcagaggtatttggtacttggaagtccatgtttgttgagtcatcttaataaatttctttgagtcgttttttatactttctcatgtgccttatgtattaagGACGGATCTGGTGCCTGCATATGCTCGTCTACTTTGTGATAATGAGGCAGAAGTTCGGATAGCAGCTGCTGGAAAAGTTACCAAGTTTTGTCGCATTTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA