Sequence
atgc intronic sequence ATGC exonic sequenceATTTGGTGCTTTCAAACAAGCTTGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgctatattcatacactcaaacgattcatgtctcattgtgagtgggaaagatttcgaatttaaaactattttatctttgttttatctgtctttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05840.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os04g26834.1 (Oryza sativa), 5'ss of exon 10
ATTTGGTGCTTTCAAACAAGCTTGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgctatattcatacactcaaacgattcatgtctcattgtgagtgggaaagatttcgaatttaaaactattttatctttgttttatctgtctttgcag
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ATCTGGTCCTTTCAAATAAGTTAGTTGTCTATGACCTGGAAAATCAAGTCATTGGCTGGACTGAGTACAACTgtaagtttaacacattcaaatttgattgttatgagttcattccatagtactttacatgtttagtctattgtt--cttgctaatgtcttgacaatccgaaaat
upper sequence: AT1G05840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: AC155377.1_FGT002 (Zea mays), 5'ss of exon 10
ATTTGGTGCTTTCAAACAAGCTTGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgcta---tattcatacactcaaacgattcat--gtctcattgtgagtgggaaagatttcgaatttaaaactattttatctttgttttat-ctgtctttgcag----------------------------
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ATCTTGTGCTTTCAAACAAGTTGGTTGTCTATGACTTGGAAAATCAAGTCATCGGGTGGACTGACTATAACTgtaagtgctaacacactcaaatctgccaattcttagtccatttcataatcaaattgcatagttggttgttctgaattatag-atgttagtcgtgtgttgccccctcaactctctggtcatctgcttgcaatttcag
upper sequence: AT1G05840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: AC190609.3_FGT004 (Zea mays), 5'ss of exon 9
ATTTGGTGCTTTCAAACAAGCTTGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgctatattcatacactcaaacgattcatgtctcattgtgagtgggaaagatttcgaatttaaaactattttatctttgttttatctgtctttgcag
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ATCTTGTCCTTTCCAACAAGTTGGTTATCTATGACTTGGAAAATCGAGTCATTGGGTGGACTGACTACAACTgtaagtgtta-gcacgttc---caatctgctcatgccctat----------atatatttc-----cacaactatttggtcatccgcctgtaaaatttcag--
upper sequence: AT1G05840.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA18G51920.1 (Glycine max), 5'ss of exon 9
-ATTTGGTGCTTTCAAACAAGCTTGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgctatattcatacactcaaacgattcatgtctcattgtgagtgggaaagatttcgaatttaaaactattttatctttgttttatctgtctttgcag--
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GATTTAGTGCTTTCAAATAAACTTGTCTTCTATGACCTTGAAAATCAGGTTATTGGATGGACTGAGTACAACtgtaagtatcattattagttctttataatcttc-tgt---attttaaataatataaatgaataatataaaacatttgtagattt-ttgtgaaaacatctataataMapped 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|86085590|gb|DR381349.1|DR381349EST: TGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACT GCTCATCAAGCATAAAAGTAAAAGACGAAGGCACAGGAACAGTTCATCTAG
genomic: TGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgcta ... gtctttgcagGCTCATCAAGCATAAAAGTAAAAGACGAAGGCACAGGAACAGTTCATCTAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTTGGTGCTTTCAAACAAGCTTGTTCTCTACGATCTCGAAAATCAGCTCATTGGGTGGACTGAATACAACTgtaagtgctatattcatacactcaaacgattcatgtctcattgtgagtgggaaagatttcgaatttaaaactattttatctttgttttatctgtctttgcag
- - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA