Sequence
atgc intronic sequence ATGC exonic sequence...tctctaataaataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttggactaatgttttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22740.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g42020.1 (Oryza sativa), 3'ss of exon 3
--tctctaata-aataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttggactaatgttttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
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ctatactagtgtagcacactggccttgttttggacttttttcttttggcatggtg-atgacatgtttgttgctgctgacggtggtgatggcgtg--tgagcagTGAATGCAAATGAATGCCTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCAAAGTAGAGCAAGAAGTGGGTTCCTCCACACACGCCTTCTT
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g09930.1 (Oryza sativa), 3'ss of exon 3
tctctaataaataattaagatttaattgagctttgtttgtcttattaaattg-tatgttttttggacta--atgtt-ttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
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-ttctcatggagctatgatgttgatcttgtctttga--actatatgatgttgacattgtctttgaactacaatgatattgatactgtcttttgt-ttctaccagTGAATGCAGATGAGTGCTTGATGACAAGGATGCAGGAGATGTCCTTGGATTACCACTTCACAGTGGAGCAGGAAGTGAGCTCCTCTGTCTGCGCATTCTT
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G19490.1 (Glycine max), 3'ss of exon 3
--tctctaataaataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttg-gactaatgttttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
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actcttttaatcattttcaccttttaattataaa--gctaatcataatatat-atacattgctaataacgtatctcttttttttttttttttttttgtgacagTGAATTCTGACGAGTGCTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCATGCTTTCTT
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G08990.1 (Glycine max), 3'ss of exon 3
tctctaataaataattaagatttaattgagc--tttgtttgtcttattaaattgtatgttttttggactaatgtttta-atcctttgttgtatacttttg---cagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
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------acagattgttactaatcattttcaccttttaattatgaagctaatcatgatatctacattgctaataagagatatctttcttcttgtttttttgtgacagTGAATTCTGATGAGTGTTTATTGACAAGAATGCAAGAGATGTCCCTGGATTACCATTTCACAGTAGAGCAAGAAGTTGGATCAGCCACTCACGCTTTCTT
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G05350.1 (Glycine max), 3'ss of exon 3
tctctaataaataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttggact--aatgttttaatcctttgttgtatacttttg-cagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
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ttttaactctaaaatctgagcatgataaaacc--attgaaaatatcaatttcaggattttttgtacttcactaatttgatcatg-gtgattggtttgtgacagTGAATGCGAATGAGTGCTTGTTGACAAGAATGCAAGAGATGTCACTGGATTATCATTTCACAGTAGAGCAAGAAGTTGGGTCAGCCACTCATGCTTTCTT
upper sequence: AT5G22740.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0061g01230.t01 (Vitis vinifera), 3'ss of exon 3
tctctaataaataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttggactaatgttttaat---cctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
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cctttccaaattggacaaaaattataataataataataataatattta--tgattggttgataaa-tgatactaaaatggatttatacgggtaattttggcagTAAATGCGGACGAGTGCTTAATGACAAGGATGCAAGAGATGTCATTGGATTATCATTTTACAGTGGAGCAAGAAGTTGGATCAGCTACTCATGCCTTCTTMapped 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|86052418|gb|DR348175.1|DR348175EST: CCTCATGCACAATCCCAACATTGCCTTGGTTCAGGCTCGATGGCGGTTCG TAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATT
genomic: CCTCATGCACAATCCCAACATTGCCTTGGTTCAGGCTCGATGGCGGTTCGgtaatcattt ... acttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATT
EST:
gi|86052419|gb|DR348176.1|DR348176EST: CCTCATGCACAATCCCAACATTGCCTTGGTTCAGGCTCGATGGCGGTTCG TAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATT
genomic: CCTCATGCACAATCCCAACATTGCCTTGGTTCAGGCTCGATGGCGGTTCGgtaatcattt ... acttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaattgtatgttttttggactaatgttttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
tactttt CT-rich tract
actaatgttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctctaataaataattaagatttaattgagctttgtttgtcttattaaattgtatgttttttggactaatgttttaatcctttgttgtatacttttgcagTAAATTCTGATGAGTGCTTATTGACGAGAATGCAAGAAATGTCATTGGATTACCATTTCACTGTTGAGCAAGAAGTGGGTTCATCAACACATGCTTTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - aaataat
- - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttttgg