Sequence
atgc intronic sequence ATGC exonic sequencegtaggttgtggtccagatctatcgtatacagtagaatcatgctttatgagaatgtcatacttttgaacgttttggtaacttaaaactgttgttttgcttgttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTTATAGATACAGGTGTACTCCCTACGCTTGTGAAGATAGTAAAGAAAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G63640.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G63640.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G38320.2 (Glycine max), 3'ss of exon 4
gtaggttgtggtccagatctatcgtatacagtagaatcatgctttatgagaatgtcatacttttgaacgttttggtaacttaaaactgttgttttgcttgttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTTATAGATACAGGTGTACTCCCTACGCTTGTGAAGATAGTAAAGAAAAAA
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--aagcttggttatttgactttcttgtgttgaatatttacatttcttgc---tttcctgttctgtagtgttttactgagtca---tctttgatcta-ttgattttctagTTGCTGGAAATGTTGATGAACAATATTGGAGAGCATATTCATGAGCAG---------------------------------------------------
upper sequence: AT5G63640.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G38320.1 (Glycine max), 3'ss of exon 4
gtaggttgtggtccagatctatcgtatacagtagaatcatgctttatgagaatgtcatacttttgaacgttttggtaacttaaaactgttgttttgcttgttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTTATAGATACAGGTGTACTCCCTACGCTTGTGAAGATAGTAAAGAAAAAA
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--aagcttggttatttgactttcttgtgttgaatatttacatttcttgc---tttcctgttctgtagtgttttactgagtca---tctttgatcta-ttgattttctagTTGCTGGAAATGTTGATGAACAATATTGGAGAGCATATTCATGAGCAGGTGATTGATACTGGAATTATTACTATTCTCGTAAAAATTGTGAAGAAAAAG
upper sequence: AT5G63640.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G16740.1 (Glycine max), 3'ss of exon 4
gtaggttgtggtccagatctatcgtatacagtagaatcatgctttatgagaatgtcatacttttgaacgttttggtaacttaaaactgttgttttgcttgttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTTATAGATACAGGTGTACTCCCTACGCTTGTGAAGATAGTAAAGAAAAAA
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--aagcttggttatttgactttcttgtgtagaatatttacattccttgc---tttcctgttctgtagtgttttactgagtca---tctttgatcta-ttgattttgtagTTGCTGGAAATGTTGATGAACAATATTGGAGAGCATATTCATGAGCAGGTGATTGATACTGGAATTATTCCTATTCTAGTAAAAATTGTGAAGAAAAAG
upper sequence: AT5G63640.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv07s0031g03190.t01 (Vitis vinifera), 3'ss of exon 2
gtaggttgtggtccagatctatcg-tatacagtagaatcatgctttatgagaatgtcatacttttgaacgttttggtaacttaaaactgttgttttgcttgttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTTATAGATACAGGTGTACTCCCTACGCTTGTGAAGATAGTAAAGAAAAAA
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-----atatggtcatgaaatggctctacatcttagca-ctcaccctgc-agttcttcatcacttttgctgtctatctgacc---atttgattagcatttgatttttgcagTTATTGGAGATGTTGATGAATAATATTGGAGAACCTGTTCACAGACAGGTGATTGATAATGGGCTCCTCCCTATACTAGTGAAGATAGTAAAGAAAAAGMapped 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|86072053|gb|DR367810.1|DR367810EST: AAAAACGCTTGGGAAGCAAGAACCCAAATACTCAATTATATGCTGTCCAG TTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTT
genomic: AAAAACGCTTGGGAAGCAAGAACCCAAATACTCAATTATATGCTGTCCAGgtaggttgtg ... gttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatacttttgaacgttttggtaacttaaaactgttgttttgcttgttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTTATAGATACAGGTGTACTCCCTACGCTTGTGAAGATAGTAAAGAAAAAA
tggtaac putative branch site (score: 2)
ttttgcttgttctt putative PPT
taacttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttgtggtccagatctatcgtatacagtagaatcatgctttatgagaatgtcatacttttgaacgttttggtaacttaaaactgttgttttgcttgttcttgcagTTGCTAGAGATGTTGATGAATAATATTGGAGAGAATATTCATAAGCAAGTTATAGATACAGGTGTACTCCCTACGCTTGTGAAGATAGTAAAGAAAAAA
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