Sequence
atgc intronic sequence ATGC exonic sequenceATCGCCTCCTGAACCGAAGGCCTCCAAGCCTAGCACACCTCCCACAGGAGATCGTGTTTTTGCTAGTCCTCTTGCAAGAAAGTTGGCTGAAGATAATAACgttagtttcacagtgttctaaatattctgttttttcttattattcctgcttaatttttcttcttgtttactttatttaaaaaaacatcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54220.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54220.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 10
ATCGCCTCCTGAACCGAAGGCCTCCAAGCCTAGCACACCTCCC---ACAGGAGATCGTGTTTTTGCTAGTCCTCTTGCAAGAAAGTTGGCTGAAGATAATAACgttagtttcacagtgttctaaatattctgttttttcttattattcct--gcttaatttttcttcttgtttactttatt-taaaaaaacatcag--------------------
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---TTCTCCAGAGCCAAAGAGTTCTAAGGCTAGTGCAGCTCCTTCAACAGAAGGTCGCATTTTTGCTAGTCCTCTTGCAAGAAAACTGGCTGAAGAACACAATgtatgttaaatacgatactgag-actaaaactttgttattcatccattaatttcatattgactaatggtgagttgattctcgtgcatcattcgattcttttccatgaaagtag
upper sequence: AT1G54220.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 5'ss of exon 9
ATCGCCTCCTGAACCGAAGGCCTCCAAGCCTAGCACACCTCCCA---CAGGAGATCGTGTTTTTGCTAGTCCTCTTGCAAGAAAGTTGGCTGAAGATAATAACgttagtttcacagtgttct-----aaatattctgttttttctt-----attattcctgcttaatttttcttcttgtttactttatttaaaaaaacatcag---------------------------------------------------------------------------------
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---TTCACCTCAGCCAAATGTTTCAAAAGCTGTTGAAAGTTCCAAAGCAGGAGATCGCATTTTTTCCAGTCCTCTTGCAAAAAAGTTAGCTGAAGATCACAATgttagtcactgcatcttttggtgtaaaaattttattactaccaccaaaataaggcccatccatgggaccttattattt-ctccatatgatgacatttaagtttgcttttgtaatgatatatattcatgaggcatttatgttttattttgatgtttaatgtaatatctctttccttattcagMapped 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|164202138|gb|ES016880.1|ES016880EST: ATCGTG-TTTTGCTAGTCCTCTTGCAAGAAAGTTGGCTGAAGATAATAAC GTGCCTCTCTCAGACATCGAAGGCACAGGTCCTGAAGGACGGAT
genomic: ATCGTGTTTTTGCTAGTCCTCTTGCAAGAAAGTTGGCTGAAGATAATAACgttagtttca ... aaaacatcagGTGCCTCTCTCAGACATCGAAGGCACAGGTCCTGAAGGACGGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATCGCCTCCTGAACCGAAGGCCTCCAAGCCTAGCACACCTCCCACAGGAGATCGTGTTTTTGCTAGTCCTCTTGCAAGAAAGTTGGCTGAAGATAATAACgttagtttcacagtgttctaaatattctgttttttcttattattcctgcttaatttttcttcttgtttactttatttaaaaaaacatcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA