Sequence
atgc intronic sequence ATGC exonic sequencegtaaggccacacgacctgctgttagatgattttgtttaagctatgaaacacatgttaagaggcaagtgttttgcttttctctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTACCGAGATGAACAAATTATGGGTTCGAATGCAACATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51310.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 4
-------gtaaggccacacgacctgctgttag--atgattttgtttaagc-----tatgaaacacatgttaagaggcaagtgttttgcttttct-ctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTACCGAGATGAACAAATTATGGGTTCGAATGCAACATCAG
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gatttttgtatgtcttgaatatggggcagtggcaattattttaaagcagcaccaatttgaaattaat-ccgatgtgtgaatgcctaatttgacaactgtagGGATGCGGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 4
-----gtaaggccacacgacctgctgtta-gatgattttgtttaagcta-------tgaaacacatgttaagaggcaagtgttttgcttttct-ctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTACCGAGATGAACAAATTATGGGTTCGAATGCAACATCAG
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ctgatgtatctgtcttgaatatggggcagtggcaattattttaaagctgcaccaattggaaattaacttgatgtgtgaatgcctattttgacaactgtagGGATGCAGATACTGTAGCAGATGCTGTAGAGTTCGTGCTCCAAAATTTCACTGAAATGAACAAACTTTGGGTGCGAATGCAACATCAG
upper sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S313_104V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------gtaaggccacacgacctgctgttagatgattttgtttaagctatgaaacacatgttaagag-gcaagtgttttgcttttctctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTACCGAGATGAACAAATTATGGGTTCGAATGCAACATCAG
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tggaggaggggatttgtttgatattttgattcgttgtgaaat--tcatgtttcgagtttcccgcacgagtcggctgtgcttgactttgaagttgaatttcagGGAGGGTGGCAACGTGATGGACGCGGTGGAGTTTGTGCTCCAGAATTTTACGGAGATGAACAAATTGTGGGTGCGGATGCAACATCAGMapped 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|19874725|gb|AU235556.1|AU235556EST: GCTCAAGTTACTAGGGATAAGTTACCCAGCATTGGTTCTGACTTGGAAGG AGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTAC
genomic: GCTCAAGTTACTAGGGATAAGTTACCCAGCATTGGTTCTGACTTGGAAGGgtaaggccac ... ttctctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTAC
EST:
gi|164064517|gb|ES178500.1|ES178500EST: CTCAAGTTACTAGGGTATAAGTTACCCAGCATTGGTTCTGACTTGGAAGG AGATGGTGATGCACAACATGAATGCTTTAGAG
genomic: CTCAAGTTACTAGGG-ATAAGTTACCCAGCATTGGTTCTGACTTGGAAGGgtaaggccac ... ttctctccagAGATGGTGATGCACA-CATGAATGCTTTAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtttaagctatgaaacacatgttaagaggcaagtgttttgcttttctctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTACCGAGATGAACAAATTATGGGTTCGAATGCAACATCAG
tgttttgcttttctct CT-rich tract
tatgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggccacacgacctgctgttagatgattttgtttaagctatgaaacacatgttaagaggcaagtgttttgcttttctctccagAGATGGTGATGCACACATGAATGCTTTAGAGTTCGTGCTTCAAAATTTTACCGAGATGAACAAATTATGGGTTCGAATGCAACATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG