Sequence
atgc intronic sequence ATGC exonic sequencegtaacaacaacacttcaaagtgctgccctaaagttaagttgcaagattttttttgatgaagtttttttttttcttgtcatagGGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAACAAACAAAGGATGACTCGAATCCTCAGATTGCACTGCTACCTTTGCATC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54870.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54870.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 3
-----------------gtaacaacaacacttcaaagtgctgccctaaagttaagttgcaagattttttttga---tgaagtttttttttttcttgtcatagGGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAACAAACAAAGGATGACTCGAATCCTCAGATTGCACTGCTACCTTTGCATC
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tttactagttatataccgtaggaaagctaatgtga--tgtttcccttggcgtgaggcgtatttatttcagcaacagtaagctaacatgcattaatttttcagGGAGAAGATATTATTGCTATCTTGCCATGGGAAGAATGGTGGGACTTTGAAGTAAAAAAGGATGATTCCAATCCTCAGATTGCATTACTACCTTTGCATC
upper sequence: AT5G54870.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 3
--------gtaacaacaacacttcaaagtgctgccctaaagtt----aagttgcaagattttttttg------atgaagtttttttttttcttgtcatagGGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAACAAACAAAGGATGACTCGAATCCTCAGATTGCACTGCTACCTTTGCATC
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tacctatggcactgggttctctccaatgtagtgcactatttctttatgagctggagcagttccaatgtccaaaattaagctaacaaatggtggattgcagGGAGAAGATGTTATTGCTATCCTGCCCTGGGAGGAATGGTGGGAGTTTGAAGTGACAAAGGATGACTCAAATCCTCAGATTGCACTGCTTCCTTTGCATCMapped 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|116450157|gb|EG492749.1|EG492749EST: ACTCTGAAGGGAAACTTTGGGTTGGTGAGTCACGAAATGAAAATGATAAG GGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAA
genomic: ACTCTGAAGGGAAACTTTGGGTTGGTGAGTCAGGAAATGAAAATGATAAGgtaacaacaa ... cttgtcatagGGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaagttaagttgcaagattttttttgatgaagtttttttttttcttgtcatagGGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAACAAACAAAGGATGACTCGAATCCTCAGATTGCACTGCTACCTTTGCATC
tttttttttttcttgt CT-rich tract
aagattttttttgatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacaacaacacttcaaagtgctgccctaaagttaagttgcaagattttttttgatgaagtttttttttttcttgtcatagGGAGAAGATGTAATAGCAATCTTACCATGGGAGGAGTGGTGGGCATTTGAACAAACAAAGGATGACTCGAATCCTCAGATTGCACTGCTACCTTTGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG