Sequence
atgc intronic sequence ATGC exonic sequenceTACTGGAGAGCCAATTGAAACCAAAAGCAGGGAAGATGTCCCAAGCAACTTTGAGAAGGCTAAAGCTCATAAATCCACAATGGAGGCTGCCATCTCCGAGgttcttgtttaatatcctgctacttgtcactggtagtgacatactaatgcatggataatcatttttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43300.2 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: LOC_Os07g37750.1 (Oryza sativa), 5'ss of exon 15
TACTGGAGAGCCAAT--TGAAACCAAAAGCAGGGAAGATGTCCCAAGCAACTTTGAGAAGGCTAAAGCTCATAAATCCACAATGGAGGCTGCCATCTCCGAGg--------ttcttgtttaa--tatcctgctacttgtcactggtagtgacat-actaatgcatggataatcatttttgcag-----------------------------------------------------------------------------------------
| | | | | | ||||| || ||| || |||| | | | ||||||| |||||||||||||| || |||||||||||||| ||||| |||| || ||||| | | | || | | | | | | || || | ||| | | || || ||| |
--GAGCATAACAAGTGATGAAATAAAGAGCCAAGAGGATGGTCGCAATCAGTTTGAGATAGCTAAAGCTCATAAGTCAACAATGGAGGCTGCAATCTCAGAGgtagggaggttgctgttttaattgttttgttttgttttatttattttgcaatcaagaatctttatctcatgatgtttaccaaatacatgcatgttcttgtagcagttaacctagtttgctgttactgcattgctgattgtaactgaagtatttttccctttccttttcag
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA17G04890.1 (Glycine max), 5'ss of exon 18
TACTGGAGAGCCAATTGAAACCAAAAGCAGGGAAGATGTCCCAAGCAACTTTGAGAAGGCTAAAGCTCATAAATCCACAATGGAGGCTGCCATCTCCGAGgttcttgtttaatatcctgctacttgtcactggtagtgacatactaatgcatggataatcat-ttttgcag--------------------------------------------------------
||||||| | ||||| | | |||||||||||| | || | |||||||||||||| ||||||||||||||| ||||||||||||| | ||||| | | | | || || | | | || || | | || | ||| || || |
AGCTGGAGATTCTTCTGAAATAAGATCCAGGGAAGATGTAACCAGTGATTTTGAGAAGGCTAAGGCTCATAAATCCACATTGGAGGCTGCCATTGCTGAGgtattgatcatgttttct-ttaatcttttttaacagggaagagatttgtcttgacttttcaccttctgttgcataatatgatcaggctattgttgggggctgacttatggttttaataatcttttag
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: GLYMA13G17610.1 (Glycine max), 5'ss of exon 18
TACTGGAGAGCCAATTGAAACCAAAAGCAGGGAAGATGTCCCAAGCAACTTTGAGAAGGCTAAAGCTCATAAATCCACAATGGAGGCTGCCATCTCCGAGgt-----tcttgtttaatatcctgctacttgtcactggtagtgacatactaatgcatggataatcattt-ttgcag--------------------------------------------------
||||||| | ||||| | | ||||||||||| | || |||||||||||||||| ||||||||||||||| ||||||| ||||| | ||||| || ||||| | | | | | || || || || || | | ||| | || |||||
AGCTGGAGATTCTTCTGAAATAAGATCTAGGGAAGATGTAACCAGTGACTTTGAGAAGGCTAAGGCTCATAAATCCACATTGGAGGCAGCCATTGCTGAGgtattgatcatgttttgtttaatctttttcaacag-ggaagggaaatttgtcttaactcttaacctcttgttgcataatgatgaagctatgttgggggctgacttatggttttaataatcttttag
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 5'ss of exon 17
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 5'ss of exon 18
TACTGGAGAGCCAATTGAAACCAAAAGCAGGGAAGATGTCCCAAGCAACTTTGAGAAGGCTAAAGCTCATAAATCCACAATGGAGGCTGCCATCTCCGAGgttcttgtttaat-----atcctgctac----ttgtcactggtagtgacatacta-atgcatggataatcatttttgcag--------------------
|| |||| || |||| | ||||||||||||||| | || | |||||||||| ||| || |||||||||||||| ||||||||||||||||| ||||| ||| | | ||| | | |||| | | || ||| | | | || | | || |
AGCTAGAGAATCAGTTGAGATAAAAAGCAGGGAAGATATGCCCAATAACTTTGAGAGGGCAAAGGCTCATAAATCCACTATGGAGGCTGCCATCTCTGAGgtaattgatcagattttaatcttatcaaaaaattgttaagattttctgcaaactctacacgacaagaagtaatgctgaaagctagaacaatattcagggtMapped 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|164234983|gb|ES059144.1|ES059144EST: GGAGGCTGCCATCTCCGAG TTCAACAGGAATTCAGTGAAAGGTGTCGAATATCTAATTGCAAACAAGTTG
genomic: GGAGGCTGCCATCTCCGAGgttcttgttt ... atttttgcagTTCAACAGGAATTCAGTGAAGGGTGTCGAATATCTAATTGCAAACAAGTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TACTGGAGAGCCAATTGAAACCAAAAGCAGGGAAGATGTCCCAAGCAACTTTGAGAAGGCTAAAGCTCATAAATCCACAATGGAGGCTGCCATCTCCGAGgttcttgtttaatatcctgctacttgtcactggtagtgacatactaatgcatggataatcatttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG