Sequence
atgc intronic sequence ATGC exonic sequence...ctagatttaatttgtttaatgactctcattagcgagacaatgataatcttttatttgcatataagctgaagaactaaagttggtggtgcaatttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56150.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G102471_T03 (Zea mays), 3'ss of exon 3
ctagatttaatttgtttaatgactctcatta-gcgagacaatgataatcttttatttgcatataagctgaagaactaaagttggtggtgcaatttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG
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ttgtggttagctaatatgat-attgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgttctgttctgtattaacagGTTCTCCTGTCAATCTGCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATG
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G102471_T05 (Zea mays), 3'ss of exon 4
ctagatttaatttgtttaatgactctcattagcgagacaatgataatcttttatttgcatataagctgaagaactaaagttggtggtgcaatttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG-----------------
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--------gatat-tgtggttatgttccttgagaacagtatgttcaagatagttttgtctgtttactgatctgtt--------ctgttctgtattaacaggttctcctgtcaatctgCTCACTGCTCACGGACCCAAACCCTGATGATCCTCTTGTCCCTGAGATTGCTCACATGTACAAGACCGACAGGGCCAAGTATGAGTCCACCGCACGCTCC
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G18310.1 (Glycine max), 3'ss of exon 4
ctagatttaatttgtttaatgactctcattagcg-agacaatgataatcttttattt--gcatataagctgaagaactaaagttggtggtgcaattt-ccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG
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---aatttaacatctaaagaaaatgtgaaagctgtggattagagccgatatttattcaagtattcagacttaattacttaa-ttattaatgcaatttgttgtagGTGCTACTTTCAATTTGCTCCCTGCTGACAGATCCCAACCCGGATGATCCTTTGGTGCCTGATATTGCTCACATGTACAAGACTGACAGAGACAAGTACG
upper sequence: AT5G56150.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g01190.t01 (Vitis vinifera), 3'ss of exon 4
ctagatttaatttgtttaatgactctcattagcgagacaatgataatcttttatttgcatataagctgaagaactaaagttg-gtggtgcaatt-----tccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG
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-----ttttatttacc-agtgaaagaaacagctgggacatagaggccatttagggtgccagaacagtaatgagtttgtgctctgtattttcaatgctggcctgcagGTGTTGCTCTCTATATGCTCGCTGCTGACGGATCCAAACCCGGATGATCCCTTGGTGCCAGAAATTGCCCACATGTACAAGACCGACAGAGCCAAATATGMapped 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|301501987|gb|HO207527.1|HO207527EST: GTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAG GTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCT
genomic: GTCTTGACATTCTGAAAGAGCAGTGGAGCCCTGCACTTACCGTATCCAAGgtgatcaaat ... atttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttttatttgcatataagctgaagaactaaagttggtggtgcaatttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG
aactaaa putative branch site (score: 2)
tttccgc putative PPT
ttatttgcatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagatttaatttgtttaatgactctcattagcgagacaatgataatcttttatttgcatataagctgaagaactaaagttggtggtgcaatttccgcagGTTCTTCTGTCGATATGCTCATTGCTGACGGATCCAAACCCTGACGATCCTTTGGTTCCTGAAATAGCGCACATCTACAAGACAGACCGAGTCAAGTACG
- - - - - - - - - - - ctctcat
- - - - - - - - - - - - - - - - -gagacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaaa