Sequence
atgc intronic sequence ATGC exonic sequencegtctgcccgttttataactccaagcatttcttatacggagggatcaaagcaatgattgttatttctgctagtttttttttttttacattttgttctgagaccatttttattttgcttccgtttttcagTGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTCGTTATTGACAACTGCTGTATGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03290.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 3
gtctgcccgttttataactccaagcatttcttatacggagggatcaaagcaatgattgttatttctgctagtttttttttttttacattttgttctgagaccatttttattttgcttccgtt--tttcagTGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTCGTTATTGACAACTGCTGTATGATG
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------------------------------gtccaccaatacatataaatgcctataaatttttggtctcaaattttattcatga-attttatt--aacacttttttttttaaaaaaaaattatttatagTGTTGCCGTGAGGTTGCAGAGAAATATCCTGAGATAACTTATGAGGAAGTTGTCATTGACAATTGCTGCATGATG
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 3
gtctgcccgttttataactccaagcatttcttatacggagggatcaaagcaatgattgttatttctgctagtttttttttttttacattttgttctgagaccatttttattttgcttccgtttttcagTGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTCGTTATTGACAACTGCTGTATGATG
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--------------------------------gtccaccaatacttaca-aatgcctagaaatttt--tggtctcaaattttattcatga-attttattattaatgct-ttttgttattatttct-agTGTTGCCGTGAGGTTGCAGAGAAATATCCTGAGATAACTTATGAGGAAGTTGTCATTGACAATTGCTGCATGATG
upper sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 3
gtctgcccgttttataactccaagcatttcttatacggagggatcaaagcaatgattgttatttctgctagtttttttttttttacattttgttctgagaccatttttattttgcttccgtttttcagTGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTCGTTATTGACAACTGCTGTATGATG
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----------------------------------gttgtctgttacaaatgcttaactttatgt-tgcataatcatttacctatgcatccta--ctaaggtgagttttctctt-----tgtgttgcagTGTTGTCGGGAAGTTGCAGAGAAGTACCCAGAGATAAAATATGAGGAAGTTGTCATTGACAATTGCTGTATGATGMapped 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|124800851|gb|EH890438.1|EH890438EST: TGCAGAAAACTGACGGTCTCTTTCTCAAG TGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTC
genomic: TGCAGAAAACTGACGGTCTCTTTCTCAAGgtctgcccgt ... cgtttttcagTGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTC
EST:
gi|124980567|gb|EL053511.1|EL053511EST: TCCACAAAGCCAACATTATGCAGAAAACTGACGGTCTCTTTCTCAAG TGTTGTCGTGAGGTTGCTGAGAAAGTATCCTGAGATCACTTACGAGGAGGT
genomic: TCCACAAAGCCAACATTATGCAGAAAACTGACGGTCTCTTTCTCAAGgtctgcccgt ... cgtttttcagTGTTGTCGTGAGGTTGCTGAGAA-GTATCCTGAGATCACTTACGAGGAGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttttttacattttgttctgagaccatttttattttgcttccgtttttcagTGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTCGTTATTGACAACTGCTGTATGATG
tttttattttgcttcc CT-rich tract
ttttttacattttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgcccgttttataactccaagcatttcttatacggagggatcaaagcaatgattgttatttctgctagtttttttttttttacattttgttctgagaccatttttattttgcttccgtttttcagTGTTGTCGTGAGGTTGCTGAGAAGTATCCTGAGATCACTTACGAGGAGGTCGTTATTGACAACTGCTGTATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG