Sequence
atgc intronic sequence ATGC exonic sequence...ttgactgacccataaaaacctttcaaagtggtaaatttacatgtgttatgtcttaacacactttttttcttcgtctttaccttttttgatgccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGACTTCGTGGTCCTCCATGGTTAAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G04460.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g32960.1 (Oryza sativa), 3'ss of exon 5
--ttgactgacccataaaaacctttcaaagtggtaaatttacatgtgttatgtcttaacacactttttttcttcgtctttaccttttttgatgccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGACTTCGTGGTCCTCCATGGTTAAAA
| | || ||| | || | | ||||| | || | | ||| | | ||| || || |||| | || || |||||||| |||| || ||| | |||| || | |||| || | ||||||||||||||||||||||||| | ||
aaacatatcagatatcaaattgggttaagttttcatatttagagatggttagcctttattttgctaatttattttctattgttttttct--tgaaaaattagATGGAATCATCTTCTAGGGTATCAAGAATCAGAAATCGAGAACTTGAGAGACTTCGTGGTCCTCCATGGCTGAAG
upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 4
ttgactgacccataaaaacctttcaaagtggt-aaatttacatgtgttatgtcttaacacactttttttcttcgtctttaccttttttgatgccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGACTTCGTGGTCCTCCATGGTTAAAA
| | |||| || |||| ||| | || |||| | | | || || | || || ||| ||| |||||||||||||||| || || |||||||||||||| || || | ||| |||||||| |||||||| |||| |||||| ||
-taaaaacattataattgttgggttaattggtgaaagagaaatttgttcatttctgtttgtgtgattgattttgctcttttctcctttcatgtcaagatagATGGATACCTCTTCTAGGATTTCAAAGATGCGTAACCGTGAACGTGAGAGGCTTCGTGGGCCTCAATGGTTGAAG
upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G43700.1 (Glycine max), 3'ss of exon 4
ttgactgacccataaaaacctttcaaagtggt-aaatttacatgtgttatgtcttaacacactttttttcttcgtctttaccttttttgatgccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGACTTCGTGGTCCTCCATGGTTAAAA
|| | ||| || |||| ||| || || ||| || ||| | || | || ||||| || ||| ||| |||||||||||||||| || || || ||||||||||| || || | ||| ||||||||||||||||| |||| |||||| ||
ttaaaaactttatatttgttgggttaaatggtgaaagataaatttgtcatttctgtttgtatgattgattttgctcttt-tctcctttcatgtcaagatagATGGATACCTCTTCTAGAATTTCAAAGATGCGTAACCGTGAACGTGAGAGACTTCGTGGGCCTCAATGGTTGAAG
upper sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0036g01130.t01 (Vitis vinifera), 3'ss of exon 5
ttgactgacccataaaaacctttcaaagtggtaaatttacatgtgttatgtcttaacacactttttttcttcgtctttacc-ttttttgatgccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGACTTCGTGGTCCTCCATGGTTAAAA
|| || | | | | || ||| | | | | || || || | | || ||||||| |||||||||| |||| ||||||||||| || || |||||||||||||| ||| || ||| ||||| || |||||||| ||||||||||| ||
-atgttgttacagtatgctagatagacaatgaaattttccttttcatttgatttttgtttctcatagttttgaactttaccattttttgatgtcaaggtagATGGATACTTCTTCTAGGATTTCAAAGATAAGGAGTCGTGAACGTGATAGGCTTCGTGGCCCTCCATGGTTGAAGMapped 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|19877662|gb|AU238493.1|AU238493EST: GGCTACAAGCTCTTGGGATTCAAGTTTGTAGAGCTACAGGGCAAGAACTG ATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGA
genomic: GGCTACAAGCTCTTGGGATTCAAGTTTGTAGAGCTACAGGGCAAGAACTGgtattaactt ... gccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtcttaacacactttttttcttcgtctttaccttttttgatgccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGACTTCGTGGTCCTCCATGGTTAAAA
tttttttctt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgactgacccataaaaacctttcaaagtggtaaatttacatgtgttatgtcttaacacactttttttcttcgtctttaccttttttgatgccaagatagATGGATACATCCTCAAGGATTTCAAAGATTCGGAATCATGAGCGTGAGAGACTTCGTGGTCCTCCATGGTTAAAA
- - - - - - taaaaac
- - - - - - - - - - - tcaaagt