Sequence
atgc intronic sequence ATGC exonic sequence...ttgcagtgaatttgatgtgtctgttgatggaataaccttccttgtttaaataccagtttttattatgatgatgattttcttttatcaaatataatgcaagGTTGATAGATGCTTTGGAGATGATGAAACAAGGAGTGAGACGACTTCTGGTTCCAAAAAGCGTTGTTTGGAGAGGTATGAGCAAGAGGTTCTCCATTCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G65320.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G65320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G47620.1 (Glycine max), 3'ss of exon 1
---------ttgcagtgaat-ttgatgtgtctgttgatggaataaccttccttgtttaaataccagtttttattatgatgatgattttcttttatcaaatataatgcaagGTTGATAGATGCTTTGGAGATGATGAAACAAGGAGTGAGACGACTTCTGGTTCCAAAAAGCGTTGTTTGGAGAGGTATGAGCAAGAGGTTCTCCATTCTT
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tttataatttgataactagtcttaatttgaacagtcctgaaccagttctctaatttgacaaacacacccttaatatc----taacttcacttcctctcat------caagGTTGATAGATGCGCTGGACATGATGAAACAAGGTGTGAAGCGTCTGCTTGTTCCAAAGAGCATAGCATGGAAGGGCATGAGCAAGCGATTCTCAGTTATC
upper sequence: AT1G65320.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G38710.1 (Glycine max), 3'ss of exon 1
ttgcagtgaatttgatgtgtctgttgatggaataaccttccttgtttaaataccagtttttattatgatg-----atgattttcttttatcaaatataatgcaagGTTGATAGATGCTTTGGAGATGATGAAACAAGGAGTGAGACGACTTCTGGTTCCAAAAAGCGTTGTTTGGAGAGGTATGAGCAAGAGGTTCTCCATTCTT
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--agttttaatttataaccagtcttaatttga--acagtccttaaccaattttctaatttgacaaaaacacccttaatatcttactttacttcctctcat-taagGTTGATAGATGCGCTGGACATGATGAAACAAGGTGTGAAGCGTCTGCTTGTTCCAAAGAGCGTAGCATGGAAGGGCATGAGCAAGCGATTCTCAGTTATCMapped 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|124918327|gb|EH992174.1|EH992174EST: GTTGTTTCTCCTGACAATACTCTATTGAAACAGGTTGATCCTGGGACTAG GTTGATAGATGCTTTGGAGATGA
genomic: GTTGTTTCTCCTGACAATACTCTATTGAAACAGGTTGATCCTGGGACTAGgtactgttac ... ataatgcaagGTTGATAGATGCTTTGGAGATGA
EST:
gi|116468794|gb|EG511386.1|EG511386EST: GTTGTTTCTCCTGACAATACTCTATTGAAACAGGTTGATCCTGGGACTAG GTTGATAGATGCTTTGGAGATGATGAAACAAGGAGTGAGACGACTTCTGGT
genomic: GTTGTTTCTCCTGACAATACTCTATTGAAACAGGTTGATCCTGGGACTAGgtactgttac ... ataatgcaagGTTGATAGATGCTTTGGAGATGATGAAACAAGGAGTGAGACGACTTCTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaataccagtttttattatgatgatgattttcttttatcaaatataatgcaagGTTGATAGATGCTTTGGAGATGATGAAACAAGGAGTGAGACGACTTCTGGTTCCAAAAAGCGTTGTTTGGAGAGGTATGAGCAAGAGGTTCTCCATTCTT
tttttattatgatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcagtgaatttgatgtgtctgttgatggaataaccttccttgtttaaataccagtttttattatgatgatgattttcttttatcaaatataatgcaagGTTGATAGATGCTTTGGAGATGATGAAACAAGGAGTGAGACGACTTCTGGTTCCAAAAAGCGTTGTTTGGAGAGGTATGAGCAAGAGGTTCTCCATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - -gaataac
- - - - - - - - - - - - - - - - - - - - - - - - aatacca