Sequence
atgc intronic sequence ATGC exonic sequencegttggtgattagctagcttttaaacaaatttttgagacaggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT4G39800.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G14670.3 (Glycine max), 3'ss of exon 2
gttggtgattagctagcttttaa-acaaatttttgagac-----aggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
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-ataatttctaacatgctgaaaacataaaattcttaaattaactatacttagtttctgaaccatgccataattaaacacgagtctta-attaatttatgcagGTGAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCTGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G31450.2 (Glycine max), 3'ss of exon 3
----gttggtgattagct---agcttttaa--acaaatttttgagacaggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
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ggacatgagtgacatgttgaaaacatataattactattaaattaattatacttactttttgaaccatgccataaacacgag-tcttaatt----aatttatgcagGTAAACCCTGATGATGTTGTGTTTGGGGGATGGGATATCAGTAACTTGAACCTGGCAGATGCCATGGCCAGGGCCAAGGTGTTTGATATCGACCTGCAGA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 3
gttggtgattagctagctttta---aacaaatttttgagacaggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
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gtaagttagtaactcaatttcattgaaaatatttgcatgtgtggaaagcattatttgatttatttatagtatgatataatt-tatattataatgatcagGTGAACCCAGATGACATTGTTTTTGGGGGATGGGACATCAGTGACATGAACCTGGCAGATGCAATGGCCAGGGCTAAGGTCCTGGACATTGATCTGCAGA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 3
gttggtgattagctagcttttaaacaaatttttgagacaggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
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---------------------------------gtaactaacaacaatca-aagatggttcttgagttttggtttcttgtat-----cacttgcagGTGAATCCCGACGATGTTGTTCTTGGGGGATGGGATATCAACAACATGAACCTCGCAGATGCCATGGAGCGAGCGAAAGTTTTGGACATGGACCTCCAGA
upper sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ27629 (Selaginella moellendorffii), 3'ss of exon 3
gttggtgattagctagcttttaaacaaatttttgagacaggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
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---------------------------------gtaactaacaacaatca-aagatggttcttgagttttggtttcttgtat-----cacttgcagGTGAATCCTGACGATGTTGTTCTTGGGGGATGGGATATCAACAACATGAACCTCGCAGATGCCATGGAGCGAGCGAAAGTTTTGGACATGGACCTCCAGAMapped 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|125116803|gb|EL166197.1|EL166197EST: TTTTAACGGTGAAGAGATCTATGCTCCTTTCAAGAGTCTCCTTCCAATG GTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAAC
genomic: TTTTAACGGTGAAGAGATCTATGCTCCTTTCAAGAGTCTCCTTCCAATGgttggtgatt ... ataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAAC
EST:
gi|47829323|gb|CK119007.1|CK119007EST: CTTTTAACGGTGAAGAGATCTATGCTCCTTTCAAGAGTCTCCTTCCAATG GTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAAC
genomic: CTTTTAACGGTGAAGAGATCTATGCTCCTTTCAAGAGTCTCCTTCCAATGgttggtgatt ... ataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
ttttaat putative branch site (score: 3)
tgtgttttaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtgattagctagcttttaaacaaatttttgagacaggttttcttcttaaagtgtgttttaattttgggatcgttgtgtggaaataaaaacagGTGAATCCGGATGATGTTGTGTTTGGAGGATGGGATATAAGTGACATGAACTTAGCAGATGCCATGGCTAGAGCCAGGGTTCTTGATATCGACTTGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG