Sequence
atgc intronic sequence ATGC exonic sequence...tgtattgaaaccgtggaagtaatgggtggtgagaaagtggtcatgcttgtatttttcttactttatatcttgtgaactgaaggagtttaatggggttcagGTCTGGAGTGGCATCCTCGTATCCCAATTACGCAAAATCACTTAATTTATGACGACTTGCCTCACATTATTATGGATCCCTATGAAGAATGCAGGGGTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G29170.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G29170.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G29100.1 (Glycine max), 3'ss of exon 2
-tgtattgaaaccgtggaagtaatgggtggtgagaaagtggtcatgcttgtatttttcttactttata---tcttgtgaactgaaggagtttaatggggttcagGTCTGGAGTGGCATCCTCGTATCCCAATTACGCAAAATCACTTAATTTATGACGACTTGCCTCACATTATTATGGATCCCTATGAAGAATGCAGGGGTCC
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atatattttacttcattttgcaatactacattatttaatgatcatggtttcaatgttcaaagattataggagttcttaatgaaaagcagtttcct----ttcagGTTGTGAATGGCATCCACGCATGAAAGCTGCTCGAAATCATTTCATTTACAATGACTTGCCTCACTTTATTATGGATTCATATGAAGAATGCCGTGATCC
upper sequence: AT1G29170.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G12240.1 (Glycine max), 3'ss of exon 2
tgtattgaaaccgtggaa----gtaatgggtggtgagaaagtggtcatgcttgtatttttcttactttatat--cttgtgaactga-aggagtttaatggggttcagGTCTGGAGTGGCATCCTCGTATCCCAATTACGCAAAATCACTTAATTTATGACGACTTGCCTCACATTATTATGGATCCCTATGAAGAATGCAGGGGTCC
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---cttcaaattttgcaatactacattatttaatgatcatggtttcaaactttcaatgttcaaagattataggagtccttaatgaacagcagtttcct----ttcagGTTGTGAATGGCATCCACGCATGAAAGCTGCTCAAAATCATTTCATTTACAATGACTTGCCTCACTTTATTATGGATTCATATGAAGAATGTTGTGACCCMapped 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|164235020|gb|EL968810.1|EL968810EST: CATATACATTTTGCATACACAGGAG GTCTGGAGTGGCATCCTCGTATCCCAATTACGCAAAATCACTTAATTT
genomic: CATATACATTTTGCATACACAGGAGgtttgttttg ... tggggttcagGTCTGGAGTGGCATCCTCGTATCCCAATTACGCAAAATCACTTAATTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgtatttttcttactttatatcttgtgaactgaaggagtttaatggggttcagGTCTGGAGTGGCATCCTCGTATCCCAATTACGCAAAATCACTTAATTTATGACGACTTGCCTCACATTATTATGGATCCCTATGAAGAATGCAGGGGTCC
atttttcttactttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtattgaaaccgtggaagtaatgggtggtgagaaagtggtcatgcttgtatttttcttactttatatcttgtgaactgaaggagtttaatggggttcagGTCTGGAGTGGCATCCTCGTATCCCAATTACGCAAAATCACTTAATTTATGACGACTTGCCTCACATTATTATGGATCCCTATGAAGAATGCAGGGGTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - ttgaaac
- - - - - - - -gaagtaa
- - - - - - - - - - - - - - - gagaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactgaa