Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctttttaaattcaatccactagatgttttggatcaatttatttcaatctttttcatctttggtctcctttgtttatgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 2
gtaagtctt-----tttaaattcaatccactagatgttttgga-tcaatttatttcaat--ctttttcatctttggtctcctttgttt-----atgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCG
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gtgagcattatggtcttaaactattttttcttattttattgaagttcatgtatggagttaacatttccttacctgttcttatttggctgcaaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 3
gtaagtctt-----tttaaattcaatccactagatgttttggatcaatttatttcaat--ctttttcatctttggtctcctttgttt-----atgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCG
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gtgagcattatggtcttaaactatttttcttattttattgaagttcatgcatggagttaacatttccttacctgttcttatttgactgcaaaatgcagGTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------gtaagtct-ttttaaattcaatccactagatgttttggatcaatttatttcaat-----ctttttcatc--tttggtctcctttgtttatgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCG
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gtaagttgtttcactgcaaccatagcttcattgaatcattgtttatatcatatttaagcagcacaattatgctccatgggaagtctattggctgtt--gcacaaacacattgcaaaactcacttgctcattaatatgattttctctgat-gtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAACCAGACTTGGAGTCCCATGTTTG
upper sequence: AT5G41340.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------gtaagtct-ttttaaattcaatccactagatgttttggatcaatttat-----ttcaatctttttcatctttggtctcctttgtttatgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCG
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gtaagttgtttcaatgcagccatagcttcattgaataattgtttatatcatatttaagcagcacaaatatgctccatgggaagtctattggctgttgcacacacacatagcaaaactcactagctcataaatatggttttctct-tatgtttagGTCTGGTTCTGTTTGCTTAGATGTTATTAGCCAGACTTGGAGTCCAATGTTTGMapped 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|164142670|gb|ES020162.1|ES020162EST: AAAATTTATCATCCTAATGTTGATGAACT GTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTT
genomic: AAAATTTATCATCCTAATGTTGATGAACTgtaagtcttt ... gtttatgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggatcaatttatttcaatctttttcatctttggtctcctttgtttatgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCG
tctttttcatctttgg CT-rich tract
atcaatttatttcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctttttaaattcaatccactagatgttttggatcaatttatttcaatctttttcatctttggtctcctttgtttatgcagGTCGGGTTCTGTTTGTTTAGATGTGATTAACCAAACTTGGAGTCCTATGTTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG