Sequence
atgc intronic sequence ATGC exonic sequenceTGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcgacacaagccttatatttctttcctaaacattaaccctttcctatttatatgtgtttgatag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G18480.1 |
intron # | 16 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA09G31920.2 (Glycine max), 5'ss of exon 8
TGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcgacacaagccttatatttctttcctaaacattaaccctttcctatttatatgtgtttgatag-----------
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TGCTGAAGATCTTGAAAGTGGTTTCATGTCAGATGTGGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgacttaacttggctgctgcaatgaaacacagcatattgaaaaatgtttcatgcattataagtttgtattagtgtcaca-gcttgacaaaattgatagcg
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA07G09890.1 (Glycine max), 5'ss of exon 16
TGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcga-cacaagccttatatttctttcctaaacattaaccctttcctatttatatgtgtttgatag---------------
|| ||||||||||||||||| ||| || ||||| ||||| ||||||||||| || || || ||||| || || |||||||| |||||||| |||||||| | | | ||||| | || | ||| | ||| | | | ||||| ||| | | ||| || | | ||
TGCTGAAGATCTTGAAAGTGGTTTCGCGTCAGATGTTGAATCTAAATACAAGAAGATATATGAGGATGATATAAATCCTTTTGCTGCATTCTCAAAAAAGgtgac---ttagcttggctgctgtaatgaaacacgacatttaaaaaatagtttcatgcattataagttt---gtatgtattagtgtcacagctttacatgtgcata
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv17s0000g03970.t01 (Vitis vinifera), 5'ss of exon 16
TGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcgacacaagcctt--atatttctttcctaaacattaaccctttcctatttatatgtgtttgatag--------
| ||||||||||| ||||| |||||||| ||||| ||||| || |||||||| || || || ||||| || || || ||||| || ||||| |||||||| | | | || | ||| | | | || | | || || | || || | || ||| |
TTCAGAAGATCTTGAGAGTGGTTTCAGCTCAGATGTTGAATCCAAGTACAAGAAGATATATGAGGATGATATAAATCCCTTTGCTGCTTTCTCCAAAAAGgttttcattcttgaactcctttgctgaatttgcaattttataacaatttatgtgtcaaacttgaaactaaagcatgattttggatttaaatcattgcttc
upper sequence: AT3G18480.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: EFJ26077 (Selaginella moellendorffii), 5'ss of exon 16
TGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcgacacaagccttatatttctttcctaaacattaaccctttcctatttatatgtgtttgatag
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AATCGATGATCTGGAAGGTGGCATGGTCTCAGATATTGAATCGAAGTACAAGAAAATTTACGAAGATGACATAAACCCTTTCGCTGCGTTTTCAAGAAAGgta---gctattccatact--taacatctattgttgc-tgatgtcttgatttggaaag--------------------------------Mapped 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|164096071|gb|ES174315.1|ES174315EST: TTCTCGAAAAAAG GAAAGAGAGCAACGGATCAAAGATTTGGGAATCAGAGATCGGATTACGCT
genomic: TTCTCG-AAAAAGgtaaaaaata ... tgtttgatagGAAAGAGAGCAACGGATCAAAGATTTGGGAATCAGAGATCGGATTACGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGTGGAAGATCTTGAAAGTGGATTCAGCTCGGATGTCGAATCAAAATACAAGAAAATTTACGAAGATGACATCAACCCTTTTGCAGCATTCTCGAAAAAGgtaaaaaataaaacattctgctatcatcgacacaagccttatatttctttcctaaacattaaccctttcctatttatatgtgtttgatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG