Sequence
atgc intronic sequence ATGC exonic sequenceTGGTGCTGGATTGGCCATGGCAACCATGGACATCATTAAATTACACGGTGGAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgtaaaaggaaccttctttctttcttcacttttgggaatcattggaatgaaaaccaattttaatagaggtttgtgtcaaaaaataag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20420.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 5'ss of exon 9
TGGTGCTGGATTGGCCATGGCAACCATGGACATCATTAAATTACACGGTGGAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgtaaaaggaacc-----ttctttctttcttcac----ttttgggaatcattggaatgaaaaccaattttaatagaggtttgtgtcaaaaaataag-----
||||| |||||||| ||||| || |||||||||||||| || || || || || || |||||||| ||||| |||||||||| ||| || ||| |||||| || | | |||||| | | || | || ||||| | | | || | || | ||| |
CGGTGCAGGATTGGCAATGGCTACAATGGACATCATTAAGTTGCATGGGGGTACGCCTGCCAATTTTCTTGATGTTGGTGGAAGTGCATCAGAGGGACAGgtataataagctgagaattctttttgtaactaccatctcatgtgaatcgcgccactaaggctgtgttcttcccccccattttcccaatccacctctctcg
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G064695_T01 (Zea mays), 5'ss of exon 9
TGGTGCTGGATTGGCCATGGCAACCATGGACATCATTAAATTACACGGTGGAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgta-aaaggaaccttctttctttcttcacttt----tgggaatcattggaatgaaaaccaattttaatagaggtttg-tgtcaaaaaataag------------------------------------------------------------
||| || |||||||||||||| |||||||| || || || || || ||||| || ||||||||||| ||||| || ||||||| ||| || ||| |||||| ||| | || | | | |||| | || | | | || | | |||| | | |||
TGGAGCAGGATTGGCCATGGCGACCATGGATATTATAAAGTTGCATGGTGGTACGCCCGCCAATTTTCTTGATGTCGGTGGAAGTGCATCAGAGGGGCAGgtataaattggttgccgttttagcgttacttgaatgtttgaccttctctatccatgttaaaccctgacgccattttgacattgtagcttaatttgccgcaggcgcatatgcctttgacagtgcttatcttgtaaaatttctattctatccag
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 9
TGGTGCTGGATTGGCCATGGCAACCATGGACATCATTAAATTACACGGTGGAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgtaaaaggaaccttctttctt-tcttcacttttgggaatc---------attggaatgaaaaccaattttaatagaggtttgtgtcaaaaaataag----
||||||||| || || ||||| |||||||| || || || |||| || ||||| || |||||||| || || ||||| |||||||||||||| ||||||| ||| || |||| | | ||| || || |||| | | || || || |||| ||||| | || | |||
TGGTGCTGGCTTAGCAATGGCTACCATGGATATAATCAAGCTACATGGGGGAACTCCTGCCAATTTTCTAGATGTTGGAGGAAATGCTTCTGAAAGTCAGgtaatgcgaattttgcttctgatgcatatatttaggcattggctttcttattgtagtagaatccttttctaattttggtttattccatatgatatttctt
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ19055 (Selaginella moellendorffii), 5'ss of exon 9
TGGTGCTGGATTGGCCATGGCAACCATGGACATCATTAAATTACACGGTGGAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgtaaaaggaaccttctttctttcttcacttttgggaatcattggaatgaaaaccaattttaatagaggtttgtgtcaaaaaataag
||| || ||| | || |||||||||||||| ||||| ||| | ||||| ||| |||| ||||| |||||||||||||| ||||| ||||| || |||||||| ||| ||| | || | | | | || || | || |
TGGAGCAGGACTCGCGATGGCAACCATGGATATCATCAAACTGCACGGAGGATCACCAGCCAACTTCCTTGACGTTGGCGGAAACGCTTCAGAAAACCAGgtaccttataccactttttctctctcg--tctagactccgtt----tgctacttctttccag------------------------
upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ13492 (Selaginella moellendorffii), 5'ss of exon 9
TGGTGCTGGATTGGCCATGGCAACCATGGACATCATTAAATTACACGGTGGAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgtaaaaggaaccttctttctttcttcacttttgggaatcattggaatgaaaaccaattttaatagaggtttgtgtcaaaaaataag
||| || ||| | || |||||||||||||| ||||| ||| | ||||| || |||| ||||| |||||||||||||| ||||||||||| || |||||||| | ||| |||| | ||| | | | | ||| | | |
TGGAGCAGGACTCGCGATGGCAACCATGGATATCATCAAACTGCACGGAGGCTCACCAGCCAACTTCCTTGACGTTGGCGGAAATGCTTCAGAAAACCAGgtacattatacca-ctttttctctctggtctagactctgtttgctacttctttccag-----------------------------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|86080088|gb|DR375845.1|DR375845EST: GAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAG GTGGTGGAAGCGTTTAAGATACTGACATCGGACGATAAAGTGAAAGCAATC
genomic: GAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgtaaaaggaa ... aaaaaataagGTGGTGGAAGCGTTTAAGATACTGACATCGGACGATAAAGTGAAAGCAATC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGTGCTGGATTGGCCATGGCAACCATGGACATCATTAAATTACACGGTGGAACACCCGCCAATTTCCTTGACGTTGGTGGAAATGCTTCTGAGCACCAGgtaaaaggaaccttctttctttcttcacttttgggaatcattggaatgaaaaccaattttaatagaggtttgtgtcaaaaaataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA