Sequence
atgc intronic sequence ATGC exonic sequenceTAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttattttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.1 |
intron # | 21 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 21
TAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttattttcgcatctttt-ttttgtttactgtgtcaatgag-------------aaaattcatcatgtggctttaaattgcctttgacttgtcatcag--------------
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CAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacag
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G443953_T03 (Zea mays), 5'ss of exon 22
TAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttattttc----gcatctttttt------ttgtttactgtgtcaatgagaa-----aattcatcatgtggctttaaattgcctttgacttgtcatcag-
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TAATCGTATTCCAGAAGCAGCACTGATGGCACGATCTTACCTTCCAAGCAAAGTTTCTGATATTGTCTCAATATGGAAAAAGGACCTCCAAAAGgtatcttcctaacgaattttttctctgcccttgttcttccttccaatcacacttcacattttcccatgcaatgaagaatctgtttctaattctcttaagc
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
TAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttatt-ttcgcatctttt--ttttgtttactgtg-------tcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcag------
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TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttctgattatttcattttgttttccatgaagcactttggttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 21
TAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttatttt---cgcatcttttttttg----tttactgtgtcaatgagaaaattcatcatg--tggctttaaattgcct----ttgacttgtcatcag---
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CAATCGGATCCCTGAGGCTGCTTTGATGGCACGGTCTTATCTTCCAAGCAAGGTCTCAGAGATAGTCGCTCTGTGGAGGAAAGACCTTAATAAGgtaacttgacattcacctactttctgcgatttaacaagcttggtaatcgaaggcatgagaaacagaatgaatttacttcaattttatgtgccataacgaaMapped 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|125261903|gb|EL275988.1|EL275988EST: CAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAG GTTAATCCAAAAGCAGCTGAATCTTTAGCTGAT
genomic: CAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttattttcg ... ttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TAACCGGATACCAGAAGCTGCTCTGATGGCACGTTCTTATCTTCCAAGCAAAGTTTCGGAGATAGTAGCTCTATGGAGGGAAGATCTCAGCAAGgttattttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcag
- - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG