Sequence
atgc intronic sequence ATGC exonic sequencegtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttttagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G01730.2 (Glycine max), 3'ss of exon 5
gtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttttagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA
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------------------------ggcactgatactgtggaagaaactgctataaattagtgctttcttagccta--aatagta-tgtgtgactgtcctttttctttttttcctccttattattcagGAATACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGATGGGAAAAGTTACAGTACAAATTTGGCATTCACTCCACCTGAATATCTGA
upper sequence: AT1G63500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 6
gtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttt-tagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA
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-----------------------tgggtggagctgtggaagaaactgctataaatttgcgtgttcttagccta----aatagtaa-gtgttgactgtcctttttcttttttccccccttgttatgcagGACTACAATCCTAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGGGATGGGAGAAGTTACAGTACAAATTTGGCGTTTACTCCACCTGAATATCTGA
upper sequence: AT1G63500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 6
gtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttttagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA
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------------------------------------gtaagt-atgttgctttttttcaat-tttatggtattttttttttctcttttagaatctttgatacattgc----tcttattaaatctcagGATGGCGATCCTAGACTTTCATGCTTTGGTATGATGAAGAATAGTAGAGATGGAAAAAGTTATAGCACAAACTTAGCCTTTACACCTCCTGAATATCTGAMapped 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|125324789|gb|EL338869.1|EL338869EST: GACGTGCACTCTACCATGACTTAAATGCTTATAGAGTTCTCTTTGATGAT GACTCAAATCCAAGACTTTCATGCTTCG
genomic: GACGTGCACTCTACCATGACTTAAATGCTTATAGAGTTCTCTTTGATGATgtaagttaag ... gtgtttttagGACTCAAATCCAAGACTTTCATGCTTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttttagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA
tgttaat putative branch site (score: 3)
tgttttt putative PPT
aatatagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttaagcttatttttattttattttgggcaagataagttaagcttatatgtttgattatttttaacgtttgtcaatgttaatgtgtgaatatagaaacatcatcatatgttttgtgtttttagGACTCAAATCCAAGACTTTCATGCTTCGGTCTGATGAAAAATAGTAGAGACGGAAAGAGTTATAGCACCAACCTGGCGTTCACTCCTCCAGAGTATCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC