Sequence
atgc intronic sequence ATGC exonic sequenceCACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacctatacatttcactggtccatgcatatgtaagccctgaatgaattaactttcagagaacatgaggactaatacatagaatgagcttctgtc...
Basic information
species | Arabidopsis thaliana |
transcript | AT4G22540.1 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os08g05870.1 (Oryza sativa), 5'ss of exon 8
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacctatacatttcactg-gtccatgca--tatgtaagccctgaatgaatt-aactttcagagaacatgagg--actaatacat----agaatgagct--tctgtc----
|| || || |||| || ||||| || |||||||| ||||| ||||||||||||||||| ||| ||||| | |||| ||| || | |||||||||||| || || | | || || || | | | | |||| || ||| | ||| ||| | ||| | | | | ||| | | | || | ||||
TACTGATTCACGGCTAAGGCCAGACCAGCGGCATCTAGAGAACGGTGAATATGAGAAGGCAAACGCGGAGAAGCTGAGGTTGGAACGACGACAAAGAATGgtatgttctctctctctctctctctgtgaaaagaactctttaagatgaacatagatttagcttgtagaaaccatcacgcagttgctgcattttgattgtaatctgctttgtcgcag
upper sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G061099_T01 (Zea mays), 5'ss of exon 9
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacctatacatttcactggtccatgcatatgtaagccc-tgaatg--aattaactttcagagaacatgaggactaatacatagaatgagcttctgtc---
|| || || ||||| ||||||||||||||||| || |||||||| || || |||||||| || || |||| || | || | | |||| | ||||| || |||||| || | || | | | | | | |||| | | | | ||| || | | | ||||| | || || |
GACGGATTCAAGGCTGAGACCAGATCAACGGCACCTGGAGAATGGGGAGTACGAGAAGGCCAATGCTGAAAAACTGCGCCTCGAGACACAGCAACGGATGgt------tgtacacattttacattgctatactttttttttctcatgaaagctacatcatgatcactgatcgactccatttctacattgtttgggcactgcttgca
upper sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA01G41940.1 (Glycine max), 5'ss of exon 9
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacctatacatttcactggtccatgcatatgtaagccctgaatgaattaactttcagagaacatgaggactaatacatagaatgagcttctgtc-----
||| || || |||||||||||||||||||||||||| |||||||| ||||| |||||||| || || ||||||||| |||| |||| |||| ||||||||||||| | | | | | | || || || || | |||| | | |||| | | || ||||| |
CACGGATTCCAGGCTCAGACCAGATCAACGGCATCTAGAGAATGGGGAATACGAGAAGGCCAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtacgtcttttctgc----tatgagcacgcattctcgttccccttgtatttgg-agttttcggggtacatacatgagggtttagagttctgttttctggcctgtg
upper sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA05G04340.2 (Glycine max), 5'ss of exon 10
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacctatacatttcactggtccatgc-atatgtaagccctgaatgaattaactttcagagaacatgaggactaatacatagaatgagcttctgtc-----
||| || || ||||| ||||||||||| |||||||| |||||||| ||||| |||||||| || | || |||||| |||| |||| ||||||||||||||| || | || ||| |||| | | | | || | || || |||| || | || | || | | | |
CACGGATTCCAGGCTGAGACCAGATCAGCGGCATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAAAAACAAAGGTTGGAAAAGAGGCAAAGAATGgtatgtt---tgaactcttccatggtttgttcgagaaacgtgcattctatctctt--cttttggatt-cttgtttgatcatgtgcttgtgaatttcttaactgtat
upper sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA11G03420.1 (Glycine max), 5'ss of exon 11
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtc---acctatacatttcactggtccatgcatatgtaagccctgaatgaattaactttcagagaacatgaggactaatacata-gaatgagcttctgtc
||| || || ||||||||||||||||||||| |||| |||||||| ||||| |||| ||| || || ||||||||| |||| |||| |||| ||||||||| ||| | | | | | ||| ||| | | ||| || | ||||| | ||| || ||| || | ||||| | |
CACGGATTCCAGGCTCAGACCAGATCAACGGGATCTAGAGAATGGGGAATACGAGAGGGCTAATTTGGAGAAACAAAGGTTGGAAAAGCGGCAGAGAATGgtatgtctgaattctgatagctttttcgtctttgctgctatgagca-tgcacgaattgtcgttccccttgtatttggagtattgggggtagatgagggttt---
upper sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G14820.1 (Glycine max), 5'ss of exon 10
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtc--acctatacatttcactggtccatgcatatgtaagc--cctgaatgaattaactttcagagaacatgaggactaatacatagaatgagcttctgtc
||| || || ||||| |||||||| || || ||||| |||||||| ||||| |||||||| || | ||||||||| |||| |||| ||||||||||||||| || | || | | | || || | | || | | | ||| ||||| | | || || | | | ||| | | ||
CACGGATTCCAGGCTGAGACCAGACCAGCGACATCTAGAGAATGGGGAATACGAGAAGGCTAATATGGAGAAACAAAGGTTGGAAAAGAGGCAAAGAATGgtatgtttgaactctttcgtgctttgttcgagaaacgtgcattctatcctttctttttacctttcgttgtaaatttggggt----tcttgtttgaccatgtgcg
upper sequence: AT4G22540.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 5'ss of exon 8
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgt-cacctatacatttcactggtccatgcatatgtaagccctgaatgaattaactttcagagaacatgaggactaatacatagaatgagcttctgtc-
||| || || || || |||||||||||||| ||||| |||||||| |||||||| ||||| || ||| |||| ||||||||| | |||| || |||||| | | || | |||| || | | | || | | ||| | | | | || | | | | | | || | | |||
CACGGATTCAAGACTTAGACCAGATCAACGACATCTAGAGAATGGAGAATATGAAAAGGCAAATGCAGAAAAACTACGGTTAGAGAAGCGGCAGAGGATGgtatgagtagctcctcctttccctatttcttcaatccat--tttattcatggcatcattgtttgatgattttattatttaaccaaattggagattcttgtgcMapped 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|125031258|gb|EL103527.1|EL103527EST: AAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATG TCGCGGCAACTTCAAGAAAGCGGTTGGAGACCGAAGATGGTTTGAGAGACA
genomic: AAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacc ... ttctctgcagTCGCGGCAACTTCAAGAAAGCGGTTGGAGACCGA-GATGGTTTGAGAGACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CACAGACTCTAGGCTCAGACCAGATCAACGGCATCTTGAGAATGGTGAATATGAGAAGGCGAACTTAGAGAAACAACGGTTAGAAAGAAGGCAAAGAATGgtacgtcacctatacatttcactggtccatgcatatgtaagccctgaatgaattaactttcagagaacatgaggactaatacatagaatgagcttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA