Sequence
atgc intronic sequence ATGC exonic sequencegtaagctcatgccgttgattggatgtatagttagtatacattctatagggttagtgtaataactttctttgatcttcaaaacattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09900.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 7
gtaagctcatgccgttgattggatgta--tagt-tagtatacattctatagggttagtgtaataact-ttctttgatcttcaaaa----cattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA
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gtaaagctctctcattcgcaagtcttacttggtgtggtgtgtgcgcatactcactcacgctataatggttatctgactgcctgaattcgctttagGTTCTTAGAAAGATCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGA
upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G014116_T02 (Zea mays), 3'ss of exon 7
--gtaagctcatgccgttgattgg-atgtatagttagtatacattctatagggtta---gtgtaataact------ttctttgat--cttcaaaacatt---agGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA
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gtacacactctctctctctctcaacatgtgtatacacttccccgccctgacagacacccatcaaccaacccctcaattatctgactaccttatttcctttgcagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAA
upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 7
gtaagctcatgccgttgattggatgtatagttagtatacattctataggg--ttagtgtaataactttctttgatcttcaaaacattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA
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gtactctc-tctcaacatgtgtatacact-ctgacacccatccaccaacccctcaattatctgactaccttaattccttca-----cagATTCTTAGGAAGATCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCGAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAA
upper sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 7
gtaagctcatgccgttgattggatgtatagttagtatacattctatagggttagtgtaataactttctttgatcttcaaaacattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA
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------gtaaagaatcttttccatgtat-----gcctttgcccttttgtttttttggagcaactctaac-aatctgcatg----tagGTCCTGAGGAAAATTTGCTGGTATTTAGTTTTGTCACCGCATGACCCAATGCAATCAAGCCTTCTTAACTCCACCTTGGAGGATAAGAATCTTTCTGAAAMapped 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|125291731|gb|EL305816.1|EL305816EST: CAGTAAAAGAAACTCCGGAGCAGTGGATTCCG GTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCA
genomic: CAGTAAAAGAAACTCCGGAGCAGTGGATTCCGgtaagctcat ... aaaacattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatacattctatagggttagtgtaataactttctttgatcttcaaaacattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA
taataactttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctcatgccgttgattggatgtatagttagtatacattctatagggttagtgtaataactttctttgatcttcaaaacattagGTCCTGAGGAAGATCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA