Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G42420.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G45700.1 (Glycine max), 3'ss of exon 3
--------------gtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgct-tagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
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tttctactactaaagtcaattgtggtatatgct-attattttgtgatgtttgtgggatttat-tcttttttataactgatttttattttcaacttgtaacagTCAATAGGTTCTCTTCAAAAGAAATATTCAATTGGATCTTTTGAATTGCTGAGTAAAACTGCTCCCATTCAAGCGCTTTTTCTTCTTATTCTTGGTCCAT
upper sequence: AT5G42420.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G00210.2 (Glycine max), 3'ss of exon 3
----------------gtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
|| | | | | | || | ||| || ||| | ||| || ||| ||| | || |||||||| ||| | ||| |||||||||||| || ||||||||||||||||| || ||||| ||| |||||||||| || || || ||||| ||| |||||| || | ||||| |
acttactactactaaagtcaattgtggtatatgct-attattttgtgatgtttgggggatttct-tcttttttataactgttttttt-ttcaacttgtaacagTCAATAGGTTCTCTTCAAAAGAAATATTCAATTGGATCTTTTGAATTGCTGAGTAAAACTGCTCCCATCCAAGCGCTTTTTCTTCTTATTCTTGGTCCATMapped 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|116465657|gb|EG508249.1|EG508249EST: GTTTTATCTGTGCTTGTGTTGCGATTTTCTCGTCATCCTTGCAGCAAATT TTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTG
genomic: GTTTTATCTGTGCTTGTGTTGCGATTTTCTCGTCATCCTTGCAGCAAATTgtaagtcttt ... tgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
atctgat putative branch site (score: 4)
ttttttccttctgtgt putative PPT
aattcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctttttgtttggtgatttggttttgaagcttgtggaattcaaatctgatcaattggtgttttttccttctgtgttgcttagTTAATAGGTTCTCTACAGAAGAAATATTCAATTGGGTCCTTTGAGTTGTTGAGTAAAACAGCGCCGATTCAAGCTTTTTCGCTTCTTGTTGTCGGTCCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT