Sequence
atgc intronic sequence ATGC exonic sequenceTTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgtttttttctccaaatcattcacatttgtaactgtcacgaaattttactttttgatggattag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26590.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g38400.1 (Oryza sativa), 5'ss of exon 3
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgtttttttctccaaatcattcacatttgtaactgtcacgaaattttactttttgatgg-attag---------------------------------------------------------------------
|| |||||||||| ||||| || | ||||| || | || ||||||||||||||||||||||||||| |||| | || || || || ||||| |||| || || | | | || | | || | || | ||| | | || | ||
CTGATGGGATATGGTTGGGCTGGCCTCTTCAGAAAGTTTCTTGTGGACTCACCTTACATGTGGTGGCCTTCAAACTTGGTACAGGTTTCACTCTTCAGgtctgtaattctgtaattacattctcatttctctgaaaactaacctgttcttaagctgtaataataataattctgtaattgaagtagtaatatgtgtgttgagatttttgattggtggctatgacaaaaaaaaatgcag
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os08g23130.3 (Oryza sativa), 5'ss of exon 4
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgt--tcgtgtttttttctccaaatcattc-------acatttgtaactgtcacgaaattttactttttgatggattag--------------------------------------------------------------------------------
||| | || ||||||||||| || |||||||||| ||||| || |||||| | |||||||||||||| |||| || || |||||| | ||||| |||| | || | || | | | ||| | |||||| ||| | | || | | ||| | |
TTGCTTGGGTATGGATGGGCCGGATTGTTCAGGAAGTACCTGGTTGACTCAGCCTACATGTGGTGGCCGTCAAACCTCGTCCAAGTCACCCTCTTCAGgtaatggtactaattaccagcagttattttgtcgaaatatttgtttctgaaa-aatatatgatgcaaatggggaatgggcaaacacaaactttattttgagcattttttttttttgcggggaaacttataagcaaaatttggaatgtttgtcacgcag
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G47140.1 (Glycine max), 5'ss of exon 2
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtg-tttttttctccaaatcattcacatttgtaactgtcacgaaattttactttttgatggattag-----------------------------
|| | || ||||||||||| || || ||||||| || ||| ||||| || || ||||||||||||||| |||| ||||| ||||| ||||| || |||| | || || | || | | |||| | ||| | || | | | | ||
ATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAGATTCCTTGTGGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAGgtatttaattattctttcttgtttgctgttttttggatatgtgaatgaaagagattctaagccaacttttaattttgggatattatgtgataatgacag
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA14G01610.1 (Glycine max), 5'ss of exon 5
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgtttttttctccaaatcattcacatttgtaactgtcacgaaattttacttttt--gatggattag-------------------------------------------------------------
|| | || ||||||||||| || || |||||||||| || || || || || ||||||||||||||| |||| ||||| ||||| ||||| || |||| | ||| || | || ||| |||| | | | ||||| ||||| ||| | |
ATGCTTGGTTATGGATGGGCTGGGATTTTCAGGAAATGTCTTGTAGATTCCCCGTACATGTGGTGGCCTTCAAACCTTGTCCAAGTGTCTCTATTCAGgtatttaaatttaact---attctttcttgtttggtgatttttggcgtttttatttttttggatatgtgaatgaaaaggattaattacatgaaacttttaattttgggatattctgtctgtgataatgacag
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0015g00890.t01 (Vitis vinifera), 5'ss of exon 2
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCT-TACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgtttttttctccaaatcattcacatttgtaactgtcacgaaattttactttttgatggattag------------------------
||| | || ||||||||||| || ||||||| ||||||||||||||||| || || ||||||||||| |||||| | || |||||||||||||| |||||| | | | | || | || | | | ||| || | | | | | | || |
TTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCCTATATGTGGTGGCCAGCAAATATGGTCCAAGTCTCTCTCTTCAGgttcatctctctcccttcctctc-cctgtctctctcactctccctccctctctccctctcattctcatgaaaagggtttttgttgaattgcag
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0015g00870.t01 (Vitis vinifera), 5'ss of exon 2
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgtttttttctccaaatcattcacatttg-taactgtcacgaaattttactttttgatggattag------------------
||| | || ||||||||||| || ||||||| ||||||||||||||||| || || ||||||||||| ||||||| || |||||||||||||| |||||| | | | || | | || | | | || || | | || | || | ||| | |
TTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAGgttcatctccctctccctctccctctccctctccctcaccctctccctctctttcattctcatgaaaatggtttttgttaaattgcag
upper sequence: AT4G26590.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv19s0015g00860.t01 (Vitis vinifera), 5'ss of exon 3
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgtttttttctccaaatcattcacatt-------------tgtaactgtcacgaaattttactttttgatggattag--
||| | || ||||||||||| || ||||||| ||||||||||||||||| || || ||||||||||| ||||||| || |||||||||||||| |||||| | | | || | | || | | | | | | ||| |||| | |||||| | |||
TTGCTTGGCTATGGATGGGCTGGCCTGTTCAGAAAATACCTAGTGGACTCCCCCTATATGTGGTGGCCATCAAATCTAGTCCAAGTCTCTCTCTTCAGgttcatctccctctccctctccctctccctctccctcttcctctctttcattctcatgaaaat--ggtttttgttaaattgcagMapped 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|164176277|gb|ES023455.1|ES023455EST: TCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAG AGCCTTACATGAGAAGGAGGAGAAGCGTGAAGG
genomic: TCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgttt ... gatggattagAGCCTTACATGAGAAGGAGGAGAAGCGTGAAGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGTTGGGATATGGATGGGCGGGTATGTTCAGGAAATACCTAGTGGACTCACCTTACATGTGGTGGCCTGCAAATCTTGTTCAAGTCTCTCTCTTTAGgttcgtgtttttttctccaaatcattcacatttgtaactgtcacgaaattttactttttgatggattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG