Sequence
atgc intronic sequence ATGC exonic sequencegtaataacaacagataacataattcccacttttttatctctagatttcaagtcagatgcttgaagagatgtctctattcattggcagGTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAGTACGAGGATTTGATGGCTGCAGGAATCATCGATCCAACAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55490.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 12
gtaataacaacagataacataattcccacttttttatctctagatttcaagtcagatgcttgaagagatgtctctattcattggcagGTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAGTACGAGGATTTGATGGCTGCAGGAATCATCGATCCAACAAAG
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---gttagatcttgttcactaa--cagaaaatcatatgttcacatgtacatctgaataacataaaagatg-----atgttttaccagGTTCTCTCTAACGATAACTTCAAGTTTGGTTACAATGCTGCAACTGGACAGTACGAGGATTTGATGGCTGCTGGTATCATTGACCCCACTAAG
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G095252_T02 (Zea mays), 3'ss of exon 6
gtaataacaacagataacataattcccacttttttatctctagatttcaagtcagatgcttgaagag-atgtctctattcattgg--cagGTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAGTACGAGGATTTGATGGCTGCAGGAATCATCGATCCAACAAAG
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gtacagttattc--taccaaaaatctcacacgtgtaccac---agttcatggcatggatctgaatcttgtgcaaacatttgctgcaccagGTCCTTTCTAACGATAACTTCAAGTATGGTTACAATGCTGCTACTGGACAGTACGAGGACTTGATGGCTGCTGGTATCATTGATCCTACTAAG
upper sequence: AT1G55490.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ32217 (Selaginella moellendorffii), 3'ss of exon 11
gtaataacaacagataacataattcccacttttttatctctagatttcaagtcagatgcttgaagagatgtctctattcattggc-agGTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAGTACGAGGATTTGATGGCTGCAGGAATCATCGATCCAACAAAG
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---------------------gttggcaaaacttcgttttcatgtgtagcgaagcgcgcttaccgacttgcatgcatggattttccagGTTTTGGCCAATGATAACTTCAACTTTGGCTACAACGCAGCCACGGGAACCTACGAGGATCTCATGGCTGCAGGAATTATCGATCCCACAAAGMapped 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|86087081|gb|DR382840.1|DR382840EST: AACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAG GTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAG
genomic: AACTAATCGCCAAGAATGCTGGTGTTAATGGAAGTGTAGTTAGCGAGAAGgtaataacaa ... tcattggcagGTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatctctagatttcaagtcagatgcttgaagagatgtctctattcattggcagGTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAGTACGAGGATTTGATGGCTGCAGGAATCATCGATCCAACAAAG
tctctattc CT-rich tract
tattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataacaacagataacataattcccacttttttatctctagatttcaagtcagatgcttgaagagatgtctctattcattggcagGTGCTTTCCAACGATAACGTGAAATTCGGTTACAATGCTGCAACCGGCAAGTACGAGGATTTGATGGCTGCAGGAATCATCGATCCAACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG