Sequence
atgc intronic sequence ATGC exonic sequencegtttggtctctatgtgctcttatattatatatagcttaaagaggtttatatagcatcgtttataatgtttttatatgcgttggtggatatatatgatcaaatagGTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGAGACCAGATTTAAAGAGAGGAGCTTTCTCTCAAGACGAAGAAAGCTTGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G26660.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G26660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G127490_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------------------------gtttggtctctatgtgctcttatattatatatagcttaaagaggtttatatagcatcgtttataatgtttttatatgcgttggtggatatatatgatcaaatagGTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGAGACCAGATTTAAAGAGAGGAGCTTTCTCTCAAGACGAAGAAAGCTTGAT
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gtatgtacaacaattttttttcttccctttggtcctcagttatcaactctcaattctccccttcttcctctgcatttttctcgttccagttgccaactgaaatctctctctctctcctgtctctcaaatacctcttggtcagttcaattacctaaattcgagaagacaaattgttg--cagGGCTCCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCTCCCAAGACGAAGAAGACCTCAT
upper sequence: AT5G26660.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G171781_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------gtttggtctctatgtgctcttat-attatatatagcttaaagaggtttatatagcatcgtttataatgttt-----------ttatatgcgttggtggatatatatgatcaaatagGTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGAGACCAGATTTAAAGAGAGGAGCTTTCTCTCAAGACGAAGAAAGCTTGAT
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gtatgtacgatgaaatttttcttcccttggtcctcagttatcaactctcaatcctccccttctcctccctctgcatttttctcatttccaattgccagctgaaacccctcttgtctctcaaatacctctcggtcagttcaattatctaaattcgagaagacaaattgttg--cagGGCTTCAAAGGTGCGGAAAGAGTTGTAGGCTGAGGTGGATAAACTATCTGAGGCCAGACCTCAAGAGAGGGGCATTCGCCCAAGACGAAGAAGACCTCATMapped 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|116417753|gb|EG460345.1|EG460345EST: CATCACTAGGCATGGTCATGGCTGTTGGAGTTCTGTCCCTAAACTCGCAG GTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGA
genomic: CATCACTAGACATGGTCATGGCTGTTGGAGTTCTGTCCCTAAACTCGCAGgtttggtctc ... gatcaaatagGTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagcatcgtttataatgtttttatatgcgttggtggatatatatgatcaaatagGTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGAGACCAGATTTAAAGAGAGGAGCTTTCTCTCAAGACGAAGAAAGCTTGAT
atcgtttataatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttggtctctatgtgctcttatattatatatagcttaaagaggtttatatagcatcgtttataatgtttttatatgcgttggtggatatatatgatcaaatagGTTTGCAAAGATGTGGAAAGAGTTGTAGACTTAGGTGGATAAATTATTTGAGACCAGATTTAAAGAGAGGAGCTTTCTCTCAAGACGAAGAAAGCTTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
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