Sequence
atgc intronic sequence ATGC exonic sequenceCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaatctgatatataagaaattgtccctcgtttgtgtccccctaattggttgcttgcttctaaacatgacaaagtgagatcgcagatttctctcttgagt...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53140.1 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 5'ss of exon 6
CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaa-tctgatatataagaaattgtccctcgtttgtgtccccctaattggttgcttgc-ttctaaacatgacaaagtgagatcgcagatttctctcttgagt---------------------------------------------------------------------------------
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CTATTGCACTCTCTGAGGATCACAAGCCAAATAGAAGCGATGAGAGGAAGCGAATTGAGAGTGCTGGTGGGGTTGTTATGTGGGCTGgtaagtcctgcttccatcaa----cacctagagtaccacacaatactacaatatctgtgttctaatctgagttgccatagatcgtgcctgtttattttggagaagtcactgacatacataggtggaggagacttgcaaattgcgactatcatcttgctgatgatggtaaatggacttttgcag
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G412937_T01 (Zea mays), 5'ss of exon 6
CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaatctgatatataagaaattgtccctcgt-ttgtgtccccctaattggttgcttgcttctaaacatgacaaagtgagatcgcagatttctctcttgagt
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CTATTGCGCTCTCTGAAGATCACAAGCCAAACAGAAGTGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAGgtaa---ggtctacattaaccacaccaagacaccaagtacacttgcttgttttcatgattcttgttgct-catagtg-----gccaattgacttctacag-
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA13G08090.2 (Glycine max), 5'ss of exon 6
CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaa--tctgatatataagaaat-----tgtccctcgtttgtgtccccctaattggttgcttgcttctaaacatgacaaagtg-agatcgcagatttctctcttgagt
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CAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagatacaatatttcaagcatataaatagcatcattcaatagttctgttaatattctatttctgccacatatagtgcaacatacaatggggatgggtc--------
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA14G31890.1 (Glycine max), 5'ss of exon 7
CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaatctgatatataagaaattgtccctcgtttgtgtccccctaattg-gttgcttgcttctaaacatgacaaagtgagatcg-cagatttctctcttgagt-
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CAAATGCTCTCTCTGAGGATCATAAACCAAATAGAAGTGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGgtgagatacaatatttcag---gcatataaatagcatcattatagttctgttgtgatattctgcttctgccacatttagtgcaacatacactggggatgggtc
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv16s0050g02570.t01 (Vitis vinifera), 5'ss of exon 6
CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaa---tctgatatataagaaattgtccctcgtttgtgtcccccta--attggttgcttgcttctaaacatgacaaagtgagatcgcagatttctctcttgagt
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CAATCCCTCTTTCTGAGGATCATAAACCAAATAGAAGTGACGAGCGAAAAAGAATTGAAAATGCTGGAGGTGTTGTGATGTGGGCAGgtaaaacttaattatgcatataaccatgatgttgttatagcagagaactattggttgtctgataatcaac-tgccatgataatttc-cttatggcttacaat---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|116416941|gb|EG459533.1|EG459533EST: CGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG GAACATGGAGAGTAGGTGGGGTGTTG
genomic: CGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaatctgat ... tacttgtcagGAACATGGAGAGTAGGTGGGGTGTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAGgtaatctgatatataagaaattgtccctcgtttgtgtccccctaattggttgcttgcttctaaacatgacaaagtgagatcgcagatttctctcttgagt
- - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtccctcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtccccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctcttg