Sequence
atgc intronic sequence ATGC exonic sequencegtactctttacaacaagctgatatattccattctgtaacttcatgcttttgaatgcatttaaagacagactaccacatgttttattcatagGTGATTTATTTCGGAGATCACTTATTTAGTGATCTAAGAGGGCCTTCAAAAGCTGGTTGGCGAACTGCTGCCATAATTCATGAGCTCGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G23890.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G23890.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G040945_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------gtactctttacaaca-agctgata-----tattccattctgtaacttcatgct-tttgaatgcatttaaagacagact----accacatgttttattc------atagGTGATTTATTTCGGAGATCACTTATTTAGTGATCTAAGAGGGCCTTCAAAAGCTGGTTGGCGAACTGCTGCCATAATTCATGAGCTCGAG
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gttggttattttgaacttaaacaagaatcagtttctgtattctcaattgtcttttctccgagtggtacagctttcactcttttttctctcccttaattccgtaccattttagaaaatttccatttgaatttctcatctcattttttgtgctatatattagGTGATATATTTTGGTGACCATCTTTTGAGTGACTTGAGAGGACCTTCAAAAGCTGGTTGGCGAACAGCTGCTGTAATTCGAGAACTTGAG
upper sequence: AT2G23890.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ33659 (Selaginella moellendorffii), 3'ss of exon 8
gtactctttacaacaagctgatatattccattctgtaacttcatgcttttgaatgcatttaa--agacagactaccacatgttt--tattcatagGTGATTTATTTCGGAGATCACTTATTTAGTGATCTAAGAGGGCCTTCAAAAGCTGGTTGGCGAACTGCTGCCATAATTCATGAGCTCGAG
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----------------------------------------------gtgtgaaggttttgcactggacag-ctttaaaatgcttaacatttgcagGTCCTGTATTTTGGAGATCACTTATTTAGTGATTTACGAGGCCCTTCAAAGGCTGGATGGCGCACGGCTGCTATAATTCGGGAGCTTGAGMapped 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|164189752|gb|ES031719.1|ES031719EST: ATGGTTGTCTTAAATCCTTCCTTGAAATCACAAAGTGGCATGGCCCTGAG GTGATTTATTTCGGAGATCAC
genomic: ATGGTTGTCTTAAATCCTTCCTTGAAATCACAAAGTGGCATGGCCCTGAGgtactcttta ... ttattcatagGTGATTTATTTCGGAGATCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttcatgcttttgaatgcatttaaagacagactaccacatgttttattcatagGTGATTTATTTCGGAGATCACTTATTTAGTGATCTAAGAGGGCCTTCAAAAGCTGGTTGGCGAACTGCTGCCATAATTCATGAGCTCGAG
ctgtaac putative branch site (score: 3)
ttttattc putative PPT
atgttttattcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactctttacaacaagctgatatattccattctgtaacttcatgcttttgaatgcatttaaagacagactaccacatgttttattcatagGTGATTTATTTCGGAGATCACTTATTTAGTGATCTAAGAGGGCCTTCAAAAGCTGGTTGGCGAACTGCTGCCATAATTCATGAGCTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC