Sequence
atgc intronic sequence ATGC exonic sequenceGCCATTGTACCTGTATGCTTTCTTGAATACATCAAGCAAATCAAGACCGTTTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattgatatttgagttttgtttcctcgtctagttatttagtatgtttatgccaaaaaggcaggaacacttcttttacatgctaacaactgtttgg...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12980.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os04g52340.1 (Oryza sativa), 5'ss of exon 7
GCCATTGTACCTGTATGCTTTCTTGAATACATCAAGCAAATCAAGACCGTTTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattgatatttgagttttgtttcctcgtctagttatttagtatgtttatgccaaaaaggcaggaac-acttcttttacatgctaacaa--ctgtttgg-----
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TCCCCTGTACCTGTACCCATTCTTGAATACTACCAGCAAGACAAGACCTTTTGAATACCTGCGACTCACCAGCCTGGGTGTCATCGGTGCACTTGTTAAGgta---attcatctatg----tagttacatgagttaatcgtttaa-acagtgatacgaacatgatatatattacaattgacacatttcagtaattctattctgccatc
upper sequence: AT5G12980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os07g37790.1 (Oryza sativa), 5'ss of exon 7
GCCATTGTACCTGTATGCTTTCTTGAATACATCAAGCAAATCAAGACCGTTTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattgatatttgagttttgtttcctcgtctagttatttagtatgtttatgccaaaaaggcaggaac-acttcttttacatgctaacaa--ctgtttgg-----
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TCCCCTGTACCTGTACCCATTCTTGAATACTACCAGCAAGACAAGACCTTTTGAATACCTGCGACTCACCAGCCTGGGTGTCATCGGTGCACTTGTTAAGgta---attcatctatg----tagttacatgagttaatcgtttaaccagtg-atacgaacatgatatatattacaattgacacatttcagtaattctattctgccatc
upper sequence: AT5G12980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g57130.1 (Oryza sativa), 5'ss of exon 5
GCCATTGTACCTGTATGCTTTCTTGAATACATCAAGCAAATCAAGACCGTTTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattgatatttgagttttgtttcctcgtctagttatttag-tatgtttatgccaaaaaggcaggaacacttcttttacatgctaacaactgtttgg------
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CCCACTGTATCTGTACCCTTTCTTGAATACTACTAGCAAGACAAGGCCTTTTGAGTACTTGAGGCTTACCAGCTTGGGTGTCATTGGCGCACTTGTGAAGgtaattgc--aagccagaactttatgaaaattatgagggatatgggtgtgtttcttgagtggaagcgtagat-----ttttaaagctagaccattttctgatctact
upper sequence: AT5G12980.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 6
GCCATTGTACCTGTATGCTTTCTTGAATACATCAAGCAAATCAAGACCGTTTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattgatatttg--agttttgtttcctcgtctagttatttagtatgtttatgccaaaaaggcaggaacacttcttttacatgctaacaactgtttgg--
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TCCATTGTACCTGTACCCTTTCCTCAACACTACCAGCAAAACGAGACCTTTTGAGTACCTAAGGCTTACTAGCTTGGGGGTCATTGGTGCTCTTGTCAAGgta---atttgtgcttggaagtttacctgaactaacatgtccattgtaatgcctctgcctctggtactagataggtgcatac-tacgcgatcaacagatctattMapped 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|19878482|gb|AU239313.1|AU239313EST: TTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAG GTTGATGATACTGAAGTGATCAGATTCCTTCTTCAAACTGAGATTGTCCCA
genomic: TTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattg ... ggtttggtagGTTGATGATACTGAAGTGATCAGATTCCTTCTTCAAACTGAGATTGTCCCA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GCCATTGTACCTGTATGCTTTCTTGAATACATCAAGCAAATCAAGACCGTTTGAGTACCTGCGGCTGACTAGCTTGGGGGTTATTGGTGCACTTGTTAAGgtatgtattgatatttgagttttgtttcctcgtctagttatttagtatgtttatgccaaaaaggcaggaacacttcttttacatgctaacaactgtttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaagg