Sequence
atgc intronic sequence ATGC exonic sequencegttaatctttatacccttcaagatttcatttgcagcatctttacgcttttttcatttaataagaaatatctcttattttgttcttataaacattataactgatatgcagTGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09560.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G05320.1 (Glycine max), 3'ss of exon 7
gttaatctttatacccttcaagatttcatttgcagcatctttacgcttttttcatttaataagaaatatctcttattttgttcttataaacattataactgatatgcagTGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
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gttaat--tcatgaagtttaactatttatgtaagtgatctgtac-----ttgaatccattgtctctgacttgttattttgtgtgtttggcc-ccattactgatg-gaagTGATAAGAAGAGCACCTCACGAGTTCAAGATTGCTTGTTTAGAG
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G19730.1 (Glycine max), 3'ss of exon 7
gttaatctttatacccttcaagatttcatttgcagcatctttacgcttttttcatttaataagaaatatctcttattttgttcttataaacattataactgatatgcagTGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
|||||||||| | | || || | | || | | |||| | || | | || |||||| | | | | || ||||| | |||||||||||| |||||||| ||||||||||| || ||||| |||
-gtaatctttat---tattatgacttgtcctttattccctggaggtggatttc---tgatgtctctgacttgttgttttgtgtgtttggccccttta-ctgatg-gaagTGATAAGAAGGGCACCTCACGAGTTCAAGATTGCTTGTTTAGAG
upper sequence: AT3G09560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G35930.1 (Glycine max), 3'ss of exon 9
gttaatctttatacccttcaagatttcatttgcagcatctttacgcttttttcatttaata-agaaatatctcttattttgttcttataaacattataactgatatgcagTGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
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-acaatc-----agccgtcacacttgtgtgtttatgatgaccagtcctgttttgttaaatatacatatctgacttgtattatgtttg--gaccct-taacttatg-gaagTAATAAGAAGGGCACCTCATGAGTTCAAGATTGCTTGTCTAGAGMapped 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|116396577|gb|EG439169.1|EG439169EST: TCCTGTGGTCATTTCACCAGATGGCCTATTTCCAGCATTGTACCGTGAAG TGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
genomic: TCCTGTGGTCATTTCACCAGATGGCCTATTTCCAGCATTGTACCGTGAAGgttaatcttt ... tgatatgcagTGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaataagaaatatctcttattttgttcttataaacattataactgatatgcagTGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
aaatatctcttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatctttatacccttcaagatttcatttgcagcatctttacgcttttttcatttaataagaaatatctcttattttgttcttataaacattataactgatatgcagTGATAAGAAGAGCACCTCATGAGTTCAAGATCGCATGTTTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG