Sequence
atgc intronic sequence ATGC exonic sequenceTGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G09090.2 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g61050.1 (Oryza sativa), 5'ss of exon 3
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaatt-ttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
||||||||| | || | || || ||||| |||||||||||||| |||||||||||||| ||||||| ||||| |||||||| | | || || | | |||| | | | | | || | ||| | | | | || ||| | || | | |||| |||| ||
CGATGGAAAGTTGGAAGTAGTGGTGCCATCATTTGTTCATTACCTGGAAGTTCTTGAAGGCTCTGATGGGGACAAATTGCCAGgtgtgtggtttcacattaccgat-----tagcatgttatagtggtcatcattagctctttgctataaattctggaaaaccatcaattgaatgaataggtctaaga-------------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA01G27250.1 (Glycine max), 5'ss of exon 3
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
|||||| |||||||| ||||| ||||| ||||||||||| ||||| || ||||| ||||| |||||||| ||||| |||||||||| |||| || | || | || ||||| | || | | |||| | || ||| || || ||| || |||| | | | | ||
TGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAGgtaaaaga-atgtggggttttag-----tatttttctta----ttgtgataggcttgggtc-catgagcttgggatat-ttatagaggatgaactatgtgcgccttcccttg-----------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G14690.1 (Glycine max), 5'ss of exon 3
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
|||||| |||||||| ||||| ||||| ||||||||||| ||||| || ||||| ||||| |||||||| ||||| |||||||||| |||| || | || |||| || ||||| | || | | |||| | | | ||||| | || | |||| | | | | | ||| |||
TGATGGGAAGCTTGAGATTGTGGTTCCGTCTTTTGTTCACTACCTTGAGGTTCTAGAAGGTGCTGATGGGGACAAAATGCCAGgtaaaaga-atgtggggtt--ttactatt---tttctta----ttgtggtaggcttgggttgat-gatgccgatgagcttgggatatttatagaggataaactatgtgctc------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0007g01790.t01 (Vitis vinifera), 5'ss of exon 3
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
||||||||||||||| || || ||||| |||||||||||||| || || || | ||||| |||||||||| || ||||| |||| ||| | | | |||| | | |||| | | | || | | | | || | ||| | || | || | || || ||
TGATGGAAAGCTTGATATAGTGGTTCCTTCTTTTGTTCATTATCTGGAGGTCTTAGAAGGTTCTGATGGAGATAAAATGCCTGgta----ataattgaaact-tttatatagaattttcctgggtaatccagtatgttaaactaaatatatccagtaagctgtttatttaattttacagactagtgtc------------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S334_25V6.1 (Physcomitrella patens), 5'ss of exon 3
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
||||| || || || ||||||||||| || ||||| |||||||| |||||| | ||||| |||||||||| ||| |||||||| || || | || || | | | |||| | | || | | | | | | ||| | || | || ||| || |
AGATGGCAAACTGGAAATTGTTGTTCCTTCCTTTGTACATTACCTGGAAGTTTTAGAAGGCTCTGATGGAGAAAAGCTGCCAGgt----gactcctctccccattccactctcattgcgttaaatgccgaagtatactactcttgtgtagatttattccaaattgatgactaatcaatggtaaccgc-------------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ23254 (Selaginella moellendorffii), 5'ss of exon 3
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
||||| || || ||||||||||| || ||||| ||||| |||||||| |||||||||||||| ||||| || || |||| ||| | | || | | | ||| | | || ||||| | | | | | || |
GGATGGGAAACTGGACATTGTTGTGCCGTCTTTCGTTCACTACCTCGATGTTCTTGAAGGAGCAGATGGGGAAAAAATGC-------AAGgtgtgttgagtcgtggagcttgatggtgctactgatttatgcttgtcctcgctgcttag---------------------------------------------------------
upper sequence: AT3G09090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: EFJ25263 (Selaginella moellendorffii), 5'ss of exon 3
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
||||| || || ||||||||||| || ||||| ||||| |||||||| |||||||||||||| ||||| || || |||| ||| | | || | | | ||| | | || ||||| | | | | | || |
GGATGGGAAACTGGACATTGTTGTGCCGTCTTTCGTTCACTACCTCGATGTTCTTGAAGGAGCAGATGGTGAAAAAATGC-------AAGgtgtgttgagtcgtggagcttgatggtgctactgatttatgcttgtcctcgctgcttag---------------------------------------------------------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|152035986|gb|AU236941.2|AU236941EST: TGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAG GTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTG
genomic: TGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagata ... aaatttctagGTTGGCCTGCTTTTCACCAGTCAAATGTGCACTCGAGTCCTCTTCTATTTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGATGGAAAGCTTGACATTGTTGTTCCATCTTTTGTTCATTACCTCGAAGTTCTTGAAGGAGCTGATGGAGACAAGATGCCAGgtacaagatatcttatcttctttacctttagctttctgaaattttattttgtgctttgttcatttgatgctgtagaatattaaggattttgaaaaggttactgatgctctcataaatttctag
- - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG