Sequence
atgc intronic sequence ATGC exonic sequencegtaggaagacttttttcttaagttgtccaacgaatatacttgtttactctaatggtaaataaatagattttgtttttatcttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08720.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G30070.1 (Glycine max), 3'ss of exon 10
gtaggaagacttttttcttaagttgtccaacgaatat--acttgtttac-tctaatggtaaataaatagattttgtttt---tatcttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG
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-tgaacatatttcttgaattatgtatacatcaatttctgagctgtgtgcattttatataatcttggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACTTTTTTGTCATCCAAGTCAACTGCTGGAACG
upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G37330.1 (Glycine max), 3'ss of exon 10
-gtaggaagacttttttcttaagttgtcca-acgaatatacttgtttactctaatggtaaataaatagattttgtttt---tatcttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG
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tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACG
upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G37330.3 (Glycine max), 3'ss of exon 10
-gtaggaagacttttttcttaagttgtcca-acgaatatacttgtttactctaatggtaaataaatagattttgtttt---tatcttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG-------------------------------
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tttttctaaacatatttcttgaattatgtatacataaattcctgagctattttatataatctaggctaagttagttaaaagtaagccactctttctacagGTATGTGATTTTGGGTTGTCACGGTTGAAGCACAACACATTTTTGTCATCCAAGTCAACTGCTGGAACGGTGAGAATATGAGAAAGTCTTTGTTATTCTG
upper sequence: AT1G08720.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv14s0030g01440.t01 (Vitis vinifera), 3'ss of exon 9
gtaggaagacttttttcttaagttgtccaacgaatatacttgtttactctaatggtaaataaatagattttgtttttatc--------ttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG
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---acccaagtattaagaacggaaaaacaacaaaaataatattctatcacagttgtggtttgacatacaatatcttcatggaccataatttatgactttgcagGTATGTGATTTTGGGTTGTCACGCCTGAAGCACAACACATTTTTGTCATCCAAATCAACTGCTGGAACGMapped 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|116426459|gb|EG469051.1|EG469051EST: GTGATCTCAAAACACCAAACCTTTTGGTTGATAACAACTGGAATGTTAAG GTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCC
genomic: GTGATCTCAAAACACCAAACCTTTTGGTTGATAACAACTGGAATGTTAAGgtaggaagac ... aaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttactctaatggtaaataaatagattttgtttttatcttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG
tactaac putative branch site (score: 0)
taatggtaaataaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggaagacttttttcttaagttgtccaacgaatatacttgtttactctaatggtaaataaatagattttgtttttatcttactaaccttgtagGTCGGTGATTTTGGGTTGTCTCGCTTAAAGCACAATACTTTTTTATCCTCCAAATCAACTGCTGGAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA