Sequence
atgc intronic sequence ATGC exonic sequenceGGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaagacaacactttgtgcctttggcgtcagttcaaattcagttttctgagctattgatctttctttagtattcatctgttcatggtaactctgtcgtgt...
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20890.1 |
intron # | 8 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 5'ss of exon 8
GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaagacaacactttgtgcctttggcgtcagttcaa-attcagttttctgagctattgatctttctttagt---attcatctgttcatggtaactctgtcgtgt
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GGCAGTACCAACTTGGAAGCAATTCAAATTCTTAAGAAAACTGGAGGGTCTCTAAAGGACTCCTTTTTGGATGAAGGgtatgtcagaattgtgt----ttgacaatatttagggagaaaatttccttcagtatccaacctttattgaccccaaacatctgttaggttcaagaataaagtag
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: LOC_Os03g42220.2 (Oryza sativa), 5'ss of exon 7
GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaaga----caacactttgtgcctttggcgtcagttcaa-attcagttttctgagctattgatctttctttagt-attcatctgttcatggtaactc-tgtcgtgt
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GGTAGCACAAACTTGGAAGCGATTCAAATTCTGAAGATACCTGGAGGATCCCTCAAGGACTCCTTTTTGGATGAAGGgtatgttcttccaaaagctgtactatcggaaatatttcaacatttgatgtcctt--caatagattagtttctaatcagtcattagt--gtgatagtttgtgcca---
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: EF517601.1_FGT012 (Zea mays), 5'ss of exon 16
GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaagacaacactttgtgcctttggcgtcagttcaaattcagttttctgagc--tattgatctttctttagtattcatctgttcatggtaactctgtcgtgt-----
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GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTTAAGGATTCCTTTTTGGACGAAGGgtatgta-----tttatgtaaaaaatgccaatt--gattcttttgaccgcacagcactaggctgcatgcaaattctctcacctagcaccaagttctttctttccgtc
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G058276_T01 (Zea mays), 5'ss of exon 7
GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaag-----acaacactttgtgcctttggcgtcagttcaaattcagttttctgagct--attgatctttctttagtattcatctgttcatggtaactctgtcgtgt
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GGTAGCACCAACTTGGAATCTATTCAAATTCTGAAGAAACCTGGAGGATCTCTCAAGGATTCATTTTTGGACGAAGGgtatgtatttatagaaaaat-tgccacttgattct-tttgaccacacagcactgggctgcatgcaaattctctcacctagcaccaaattctcct--ttctgtca---
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 5'ss of exon 9
GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaagaca-acactttgtgcctttggcgtcagttca---aattcagttttctgagctattgatctttctttagtattcatctgttcatggtaactctgtcgtgt
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GGCAGCACAAACTTGGAGTCTATTCAAATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGGgtagagcatataaactatgaacttcatattgtattattcagtttacatgtttaacagaagaacgaagcatcatcagtcgttt-tgtagactaagtacacaa---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|116444514|gb|EG487106.1|EG487106EST: ATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGG GTTTATTCTTGACAAGAAAATAGGAATTGGGCGGCCTAAGCGCATAGAGAA
genomic: ATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaagacaac ... atgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGAAGCACAAACTTGGAAGCTATTCAGATCATCAAAAAACCTGGAGGGTCTCTGAAGGATTCGTTTTTGGATGAAGGgtaagacaacactttgtgcctttggcgtcagttcaaattcagttttctgagctattgatctttctttagtattcatctgttcatggtaactctgtcgtgt
- - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctgtcg