Sequence
atgc intronic sequence ATGC exonic sequenceGGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatactgtttcttattatcgttttctgcggaaatttagcggagggtcaagatcctgagagaaagtgattgatttatattcttctttttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G11880.1 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 7
GGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatactgtttcttattatcgttttctgcggaaatttagcggagggt---caagatcctgagagaaagtgattgatttatattcttctttttgcag----------------------------
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GGAGCTGGTTTGGTGGTTCATGACGCAGGAGCCTACTGCATGAGCATGGCTTCAACCTACAACTTGAAGTTGCGACCACCTGAATATTGGgta-caa-actgacctatatatttttcatccgaaatcatttgttgataggttttcaaaatgctccctttatgcaat--gtttataattgttggttcccatccaatatgccctgttatttgtaatgcag
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 7
GGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatactgtttcttattatcgttttctgcggaaatttagcggagggtcaagatcctgagagaaagtgat-tgatttatattcttctttttgcag-------
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GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCACCGGAATACTGGgtac--acactacaacacacatttgctgcccagtggggacgggc--accctcattagc-taaaatatcatgttgcaatatataaaaaaatcatcacaaaaaatca
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G090722_T02 (Zea mays), 5'ss of exon 7
GGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatactgtttcttattatcgttttctgcggaaatttagcggagggtcaagatcctgagagaaagtg----attgatttatattcttctttttgcag-----
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GGAGCTGGACTGGTTGTTCATGATGCAGGTGCCTACTGCATGAGCATGGCTTCCACCTACAACCTGAAGTTGAGGCCGCCAGAGTACTGGgtac--acactacaattcatatttggtgcccattggggtctggcgcctcattaa----ctaaaatatcatgttgcaatatttcaaaagaccattaacataaatcat
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA13G20390.1 (Glycine max), 5'ss of exon 8
GGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatactgtttctt----attatcgttttctgcgga--aatttagcggagggtcaagat---cctgagagaaagtgattgatttatattcttctttttgcag
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GGTACCGGTCTGGTTGTTCATGATGCTGGTGCTTATTGTATGAGTATGGCATCAACTTACAATCTAAAGATGCGGCCTCCTGAGTATTGGgtatgaa-actgcttcttttcaattgctaatttcattggactggcttcttttatgttgagggtagctattagaggaatttacatgttgacaaccattaatg-----
upper sequence: AT5G11880.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA10G06090.1 (Glycine max), 5'ss of exon 10
-------GGAGCTGGTCTGGT---GGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatactgtttcttattatcgtttt---ctgcggaaatt-tagcggagggtcaagatcctgagagaaagtga---ttgatttatattcttctttttgcag---------------------------------------------------------
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CCCAGCAGATGCTGAGATAGCAAAGTTTGATGTTCTTGGTCCTGTCTGTGAGTCTGCAGATTTCTTTGGAAAAGATAGACAACTTCCAACTCCAGCCAAGgtaaaaatatttccttaaatatctgaactaaactatgatgatgacaattcctacttgattttactatctgaactgagtttcactttgcatggtactcttgtctggtcgttcatgatgctggtgcttattgtatgagtatggcatcaacctacaatttaaagMapped 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|86082712|gb|DR378471.1|DR378471EST: TGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGG GTTGAAGAAGATGGGTCGATCACTAAGATCAGGCATGCTGAGACATTCGAT
genomic: TGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatac ... ctttttgcagGTTGAAGAAGATGGGTCGATCACTAAGATCAGGCATGCTGAGACATTCGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAGCTGGTCTGGTGGTTCATGACGCTGGTGCATACTGTATGAGTATGGCTTCCACTTACAATCTCAAGATGCGTCCCCCGGAATACTGGgtaacaatactgtttcttattatcgttttctgcggaaatttagcggagggtcaagatcctgagagaaagtgattgatttatattcttctttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG