Sequence
atgc intronic sequence ATGC exonic sequencegccagtgtataccataacctgaataaactggattaatgtatcatctcgcaaagttacaacgtttttgtttcaactgtagTGGGCTGAAGCTATAGAAAGTATTGATCATGGAGATCCAGGATCAGAGAAGAGCTTTGGCATGAAACAAAGGCCTGATGGTGATATCGAGATTGACGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G09230.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G09230.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G16260.1 (Glycine max), 3'ss of exon 5
-------gccagtg-tataccataac--ctgaataaactg-------gattaatgtatcatctcgcaaa-gttacaacgtttttgtttcaactg---tagTGGGCTGAAGCTATAGAAAGTATTGATCATGGAGATCCAGGATCAGAGAAGAGCTTTGGCATGAAACAAAGGCCTGATGGTGATATCGAGATTGACGAAA
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tcattttatcaatgctttaatgtagtagttggagattttgtttctctaaacaatatggcagcatgcatctgttctgagtttcccttttctgataaaccagTGGGCAGAAGCAATTGATAACTTGGACCATGGAAACCCTGGATCAGATAAGAGCTTTGGCATGAAACAAAGACCTGATGGTGATATTGAGATTGATGAAA
upper sequence: AT5G09230.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G38730.1 (Glycine max), 3'ss of exon 7
----------------gccagtgtataccat-aacctgaataaactggattaatgtatcatctcgcaaa-gttacaacgtttttgtttcaactg---tagTGGGCTGAAGCTATAGAAAGTATTGATCATGGAGATCCAGGATCAGAGAAGAGCTTTGGCATGAAACAAAGGCCTGATGGTGATATCGAGATTGACGAAA
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ttaaaagcaaaaatatgttgcttcattttatcaatgtttatttctcaaaacaataagactgtgtgcatctattctgagtttcccttttctgataaaccagTGGGCAGAAGCAATCGATAACTTGGACCATGGAAACCCTGGATCAGATAAGAGTTTTGGCATGAAACAAAGACCTGATGGTGATATTGAGATTGATGAAA
upper sequence: AT5G09230.4 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv07s0031g02510.t01 (Vitis vinifera), 3'ss of exon 8
-------------------gccagtgtataccataacctgaata---aactggattaatgtatcatctcgcaaagttacaacgtttttgtttcaactgtagTGGGCTGAAGCTATAGAAAGTATTGATCATGGAGATCCAGGATCAGAGAAGAGCTTTGGCATGAAACAAAGGCCTGATGGTGATATCGAGATTGACGAAA
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tattgtatttatgttggatttaaacttgtatcttctcttggattttcattttggataagttatagattagtgggaaaataatatatgt-tttattcttcagTGGGCAGCAGCAATTGAAAACCTGAAGCATGACAGCCCTGGGTCAGACAAGAGCTTTGGGATGAAGCAAAGGCCTGATGGTGATATCGAGATTGATGAAAMapped 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|86077600|gb|DR373357.1|DR373357EST: CTTTTCCCCGAGACTTGTTTCAGGATCAGCTAAAAGCAATCAATCCTAAG TGGGCTGAAGCTATAGMAAGTATTGATCATGGAGATCCAGGATCAGAGAAG
genomic: CTTTTCCCCGAGACTTGTTTCAGGATCAGCTAAAAGCAATCAATCCTAAGgccagtgtat ... tcaactgtagTGGGCTGAAGCTATAGAAAGTATTGATCATGGAGATCCAGGATCAGAGAAG
EST:
gi|125099856|gb|EL155512.1|EL155512EST: CTTTTCCCCGAGACTTGTTTCAGGATCAGCTAAAAGCAATCAATCCTAAG TGGGCTGAAGCTATAGAAAGTA
genomic: CTTTTCCCCGAGACTTGTTTCAGGATCAGCTAAAAGCAATCAATCCTAAGgccagtgtat ... tcaactgtagTGGGCTGAAGCTATAGAAAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactggattaatgtatcatctcgcaaagttacaacgtttttgtttcaactgtagTGGGCTGAAGCTATAGAAAGTATTGATCATGGAGATCCAGGATCAGAGAAGAGCTTTGGCATGAAACAAAGGCCTGATGGTGATATCGAGATTGACGAAA
gattaat putative branch site (score: 3)
tttttgtttc putative PPT
attaatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccagtgtataccataacctgaataaactggattaatgtatcatctcgcaaagttacaacgtttttgtttcaactgtagTGGGCTGAAGCTATAGAAAGTATTGATCATGGAGATCCAGGATCAGAGAAGAGCTTTGGCATGAAACAAAGGCCTGATGGTGATATCGAGATTGACGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT