Sequence
atgc intronic sequence ATGC exonic sequencegtgggattttctttaagctgggtagctcttacgcttaataatatccacgtgaaataatctgcttctgttgattctgcatgcagGATGATGACCTGTCCAAATCAGTTGTAGCTTGTAAGAAAGAAGCAGAAGTTATCAAGACGTGGATTAATTTTCTTGAGGATACATGGCTTCTTCAGTGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13560.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13560.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G43840.1 (Glycine max), 3'ss of exon 12
-------------------gtggg-attttctttaagctgggtagctcttacgcttaataatatccacgtgaaataatctgc--ttctg--ttgattctg-catgcagGATGATGACCTGTCCAAATCAGTTGTAGCTTGTAAGAAAGAAGCAGAAGTTATCAAGACGTGGATTAATTTTCTTGAGGATACATGGCTTCTTCAGTGCT
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gtttgaggttctatttttcatggctgtgaattgttaaatcaatgttcctgaatagtgttactctcagcatcctgttgtctgaaattttgacttgaccttgattcacagGAAGATGAACTTTCAAAATCAATCAGCTCATGTAGGGTTGAAGCAGATGTTATCAAAACCTGGATTAATTTTCTGGAAGATACTTGGGTTCTTCAGTGGT
upper sequence: AT5G13560.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G38530.1 (Glycine max), 3'ss of exon 12
----------------------gtgggattttctttaagctgggtagctcttacgcttaataatatccacgtgaaataatctgc--ttctg--ttgattctgcatg-cagGATGATGACCTGTCCAAATCAGTTGTAGCTTGTAAGAAAGAAGCAGAAGTTATCAAGACGTGGATTAATTTTCTTGAGGATACATGGCTTCTTCAGTGCT
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gtttgaggttctatttttcatggctgcgtattgttaaagcaatgt--tcctgaatagtgttactctcagcatcctgttgtctaaaattttgatttgaccttgattgacagGAAGATGAACTTTCAAAATCAGTTAGCTCATGTAGGGTTGAAGCAGATGTTATCAAAACCTGGATTAATTTTCTGGAAGATACTTGGGTTCTTCAGCGGTMapped 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|125198664|gb|EL213618.1|EL213618EST: CCTGAAAACGAAG GATGATGACCTGTCCAAATCAGTTGTAGCTTGTAAGAAAGAAGCAGAAGTT
genomic: CCTGAAAACGAAGgtgggatttt ... ctgcatgcagGATGATGACCTGTCCAAATCAGTTGTAGCTTGTAAGAAAGAAGCAGAAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacgcttaataatatccacgtgaaataatctgcttctgttgattctgcatgcagGATGATGACCTGTCCAAATCAGTTGTAGCTTGTAAGAAAGAAGCAGAAGTTATCAAGACGTGGATTAATTTTCTTGAGGATACATGGCTTCTTCAGTGCT
ttaataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggattttctttaagctgggtagctcttacgcttaataatatccacgtgaaataatctgcttctgttgattctgcatgcagGATGATGACCTGTCCAAATCAGTTGTAGCTTGTAAGAAAGAAGCAGAAGTTATCAAGACGTGGATTAATTTTCTTGAGGATACATGGCTTCTTCAGTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT