Sequence
atgc intronic sequence ATGC exonic sequenceGAAACTGAGCATCATTCCTCAAGAACCAACTCTTTTCCGTGGCTGCATAAGGACAAACCTTGATCCTTTAGGTGTTTACTCCGACGATGAAATATGGAAGgtgaaataacaaacaaagactgagatttccaaatcaaaagatataaaatctttctgataaaaccattctttttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21250.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G20770.2 (Glycine max), 5'ss of exon 8
GAAACTGAGCATCATTCCTCAAGAACCAACTCTTTTCCGTGGCTGCATAAGGACAAACCTTGATCCTTTAGGTGTTTACTCCGACGATGAAATATGGAAGgtgaaataacaaac---aaagactgagatttccaaatcaaaaga-----------tataaaatctttctgataaaaccattctttttgcag----------------
||| || |||||||| ||||||||||||||||||||| ||| |||| ||||| ||| | || ||| |||| | ||||| || |||||||||||| ||||||| ||| | | || | | | | || ||| | ||| | |||| |||| || || | |
GAAGCTAAGCATCATCCCTCAAGAACCAACTCTTTTCAAGGGCAGCATTAGGACCAACTTGGACCCTCTAGGCCTGTACTCAGATGATGAAATATGGGAGgtgaatgaactagctctgcagttgaaaaatgttatatttaaataccattctcttctatgtgagcttttcaataagctcaggtttggttatgtttaatttgtatatag
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G20780.1 (Glycine max), 5'ss of exon 10
GAAACTGAGCATCATTCCTCAAGAACCAACTCTTTTCCGTGGCTGCATAAGGACAAACCTTGATCCTTTAGGTGTTTACTCCGACGATGAAATATGGAAGgtgaaataacaaaca--aagactgagatttccaaatcaaaagatataaaatctttctgataaaaccattctttttgcag---------------------------
|| || |||||||||||||||||||||||||||||| ||| |||| | | ||| | || ||| || | | ||||| || ||||||||||||||||| || ||| | | | ||| | | | | | || | | | ||||| || | |||| | |||
AAAGCTAAGCATCATTCCTCAAGAACCAACTCTTTTCAAGGGCAGCATTCGAAAGAACTTGGACCCTCTATGCCTGTACTCTGATGATGAAATATGGAAGgtaaatcaactggctctacaattgaaaaaac-atgtaataaattgaattgtttttctc-tatttctattcactaagcaaaggttttgtgggctttcatttttacag
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G01380.1 (Glycine max), 5'ss of exon 16
---------------------GAAACTGAGCATCATTCCTCAAGAACCAACTCTTTTCCGTGGCTGCATAAGGACAAACCT---TGATCCTTTA-----GGTGTTTACTCCGACGATGAAATATGGAAGgtgaaataacaaacaaagactgagatttccaaatcaaaagatataa-aatctt----tctgataaaaccattctttttgcag
|||||| |||||||| ||||||||||||||||||||| | ||| |||| || || ||| |||| | || |||| | | | | | | ||||| | | | | | ||| || || | | | | | || || | | | || | | | | || ||
GGGGTTGAAGGATTTGAGAATGAAACTAAGCATCATCCCTCAAGAACCAACTCTTTTCAGGGGCAGCATTAGAACCAACTCAGATGATGATATATGGAAGgtgaatgagctagccttccagt-tggaaaat-atgttatatttaaatacctttatcttctatgtgagcttttcaataagcacaggattggttatgtttaatttgtatgtag
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G20360.1 (Glycine max), 5'ss of exon 9
GAAACTGAGCATCATTCCTCAAGAACCAACTCTTTTCCGTGGCTGCATAAGGACAAACCTTGATCCTTTAGGTGTTTACTCCGACGATGAAATATGGAAGgtgaaataacaaa-caaagactgagatttccaaatcaa--aagatataaaatctttctgataaaaccattctttt--tgcag-----------------------------
|||||| |||||||| ||||||||||| ||||||||| ||| |||| ||||| ||||| || ||| |||| | || ||| |||||||||||||||||||| || | | | ||||| | | | ||| || | |||| | | | | ||||| | |||||
GAAACTTAGCATCATCCCTCAAGAACCTACTCTTTTCAAGGGCAGCATTAGGACCAACCTGGACCCTCTAGGCCTCTATGACGATGATGAAATATGGAAGgtgaatgaatagctccacaactgaaaaatttgtaacaagtaaatcttgttatctctttcacgag-tcattcaataagtgcagcttttataaaatttgatttgtatatttag
upper sequence: AT3G21250.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA07G01390.1 (Glycine max), 5'ss of exon 10
GAAACTGAGCATCATTCCTCAAGAACCAACTCTTTTCCGTGGCTGCATAAGGACAAACCTTGATCCTTTAGGTGTTTACTCCGACGATGAAATATGGAAGgtgaaataacaaacaaag--actg--agatttccaaatcaaaagata-----taaaatctttctgataaaaccattcttt-ttgcag-------------
|| || |||||||| ||||||||||||||||||||| || |||| || || ||| | || ||| |||| | ||||| || ||||| ||||||||||||| | | | | | || | || | ||| ||||| | | | || | | ||||| || ||
AAAGCTAAGCATCATCCCTCAAGAACCAACTCTTTTCAAGGGAAGCATTAGAACCAACTTGGACCCTCTAGGCCTGTACTCAGATGATGATTTATGGAAGgtgaatgagctagctttgcagttggaaaatatgttaatttaaagaggagtgctggcaacacactctctagcttactctttcttacacacatttcttatagMapped 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|164032314|gb|ES157053.1|ES157053EST: CTCCGACGATGAAATATGGAAG GCTCTAGAGAAGTGTCAGCTCAAGACAACGATTAGCAATCTT
genomic: CTCCGACGATGAAATATGGAAGgtgaaataac ... ctttttgcagGCTCTAGAGAAGTGTCAGCTCAAGACAACGATTAGCAATCTT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GAAACTGAGCATCATTCCTCAAGAACCAACTCTTTTCCGTGGCTGCATAAGGACAAACCTTGATCCTTTAGGTGTTTACTCCGACGATGAAATATGGAAGgtgaaataacaaacaaagactgagatttccaaatcaaaagatataaaatctttctgataaaaccattctttttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG