Sequence
atgc intronic sequence ATGC exonic sequencegtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G27650.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
--------------gtactgatt--gcagtgacaaggtc----cattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaatt-ctgttcttgtttactttattgtc-ttgtttgg-cagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT
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gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctcttgcggtgattgtatttgacttattagctatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG
upper sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
gtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT
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--------------------------------------------------------tggttagcagctacatattttaagactttaatttatat--ttttaactgaagaa-cacatattgctatatagatgg-catcctgatgtatcattttcta----------------aacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG
upper sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G36200.1 (Glycine max), 3'ss of exon 7
gtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT
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-----------------------------------------------------------attaaatacatgttcttcttgttgatagtctagttaacttttggcatgtaattgtg-------tcattgcaatgaattgatttgtcttattat----------gtctaataaaacagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA
upper sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
gtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattc--atccaattctgttcttgtttactttat---tgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT
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--------------------------------------------------------------------------------tggttgatttctgtgggtaaccacaaacac-tggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAAMapped 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|125196930|gb|EL211884.1|EL211884EST: CTAATGCAAGAAGGACTGGCAC-AATCTTCCTTGTGGGCAGAAG TGTGACAAGTAGCCGTGC
genomic: CTAATGCAAGAAGGACTGGCACAAATCTTCCTTGTGGGCAGAAGgtactgattg ... tgtttggcagTGTGACAAGTAGCCGTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT
tcttgttt CT-rich tract
ttgtttactttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattcatccaattctgttcttgtttactttattgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA