Sequence
atgc intronic sequence ATGC exonic sequenceTTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23640.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os07g23880.1 (Oryza sativa), 5'ss of exon 8
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
| | | | ||| | |||||||||| |||||| ||||| || | || |||||||||||||| ||||||||||||||||| ||||| ||||||||||||||| | | || ||| || | ||||| ||| ||| | | |||| | || || | || | | | |||||| | |||
TAAAAGAACTCGCACCTGGTGGGCTAGTTTGGTAAAGGATTTCATCTCCAATGGTGTTGATGGAATATGGAATGATATGAACGAGCCTGCTGTTTTCAAAgta---tatgatctatcatg-agtcacttatttgtatgtcat--gcagttccatttcccttagttactgtaactaatgctgtcaacttacag
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os07g23944.1 (Oryza sativa), 5'ss of exon 8
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
| | ||| ||||| |||||| || || || | | | || || || ||| | |||||||| ||||||||||||||||||| || |||||||| || ||| | || | | || || | |||| || ||| ||||| || || ||| | ||||||| |||||
TGAAAGAGCCCGCTCCTGGTGGTCTGGCTTAGTAAGGCAGTTCGTCTCTAATAGCGTTGATGGATTATGGAATGATATGAATGAACCTGCTGTTTTTAATgta---catgatctgccataaat-catttgttttatttcaactggtttcatcttgctcttctcttacattggaagtgtttgtca-catccag
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: AC212404.3_FGT006 (Zea mays), 5'ss of exon 2
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
| ||| |||| |||||||||||| |||||| ||||| || | || | |||||||||||| |||||||||||||||||||| || ||||||||||||||| | || ||| || ||| || | ||| ||| | || || | || || | | | |
TGAAAAAACACGAGCTTGGTGGGCTAGTTTGGTAAAGGACTTCATCTCTATTGGTGTTGATGGAATATGGAATGATATGAATGAACCTGCTGTTTTCAAAgta---cgtgatctatcatga---cacataattaatatggattgttcaaatttccttcgtaactgaatgtgctggtctaaacttgtag----
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: AC203753.4_FGT006 (Zea mays), 5'ss of exon 4
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
| || ||||| |||||||||||| |||||| ||||| || | || |||||||||||||| |||||||||||||||||||| || ||||||| |||||| | || ||| | | | || || || || | || | || | || || | | | |
TGAAAAGGCACGAGCTTGGTGGGCTAGTTTGGTAAAGGACTTCATCTCCAATGGTGTTGATGGAATATGGAATGATATGAATGAACCTGCTGTTTCTAAAgtacgcgatctatcatgacacatataattaatattgcattgtt--caattttttctacgtaactgaatgtgttggtctaaacttgtag----
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA04G14810.1 (Glycine max), 5'ss of exon 8
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatcttt-atccaaatttcatat------ggtcat-atttgtca-atgtccag--------------------------
|| |||| || | |||||||| ||||| ||||| || || || | |||||||||||||||||||||||||||||||| || |||||| | || || |||||| | || | | || | | || | | || | ||| ||| |||||||| | || | | || | |||||| || ||||
GTCTAAAGTTCGTGCATGGTGGGCAAATTTAGTTAAAGACTTCATTCCCAATGGTGTTGATGGTATATGGAATGATATGAACGAACCAGCTATCTTTAAGgtaattcta---atctctttggtttcttttcttcaaataatatgaaacaatatttgatccaaatcttattttttgtggatcttgatttgtttcatttccaacttctttacccatttcttttttctag
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv02s0033g01410.t01 (Vitis vinifera), 5'ss of exon 9
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
|| ||||| || || |||||||| ||| || || || ||| |||| ||||||||||||||||||||||||||||||||||| ||||||||||| || || |||||| | || || ||| | | || |||| ||| |||||| | |||| || | | || |||
GTCAAAAGCTCGTTCATGGTGGGCCTGTTTAGTCAAAGATTTTATTTCTAATGGTGTTGATGGTATATGGAATGATATGAATGAACCAGCTGTTTTTAAGgtgatttttcaaat--tcctttctcaatttcttgcatttccttttgttgctcttta-----gtctcat-tgtttttgcttttcag-------
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv02s0087g00050.t01 (Vitis vinifera), 5'ss of exon 2
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
|| ||||| || || |||||||| ||| || || || ||| |||| ||||||||||||||||||||||| ||||||||||||||| ||||||| || || |||||| | || || ||| | | || |||| ||| ||||| | ||| ||| | | || |||
GTCAAAAGCTCGTTCATGGTGGGCCTGTTTAGTCAAAGATTTTATTTCTAATGGTGTTGATGGTATATGGAACGATATGAATGAGCCAACTGTTTTTAAGgtgatttttcaaat--tcctttctcaatttcttgcatttcctttcattgctctttg-----gtctca-atgtttttgcttttcag-------
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S60_162V6.1 (Physcomitrella patens), 5'ss of exon 8
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag----------
|| ||||| |||||||| ||| | || ||||| |||| ||||| |||||||| ||||||||||||||||| ||||| ||||| || || | | || || || | | |||| |||||| | ||| | | || | ||| | | |||
CAAGAAGACACGCAAATGGTGGGCAAATCTTGTGAAGGATTTTGCAGACGTAGGTGTGGATGGTATTTGGAATGATATGAATGAACCAGCCGTTTTTAAGgt--tggaatctacttttggcttgaatgctttcagattttcaagaataaattggaacacttatgacttataatttagccattttatgcttgttctaattgtg
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ13747 (Selaginella moellendorffii), 5'ss of exon 8
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgta--attttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
|||| || | |||||| ||| || | || || || ||||| || || || |||| ||||||||||||||||| ||||| ||||||||||| ||| | | | | || | || |||| ||| | || | | |||
AAAGAAAGTCCGTGCATGGTGGAGTAACCTGATAAAAGACTTCGTTTCTAACGGAGTCAATGGCATATGGAATGATATGAACGAGCCCGCTGTTTTCAAGgtacaaatgtgtttaaaaaatgagttcaa--gtttaaacttacgtaagctaatgcag-------------------------------------
upper sequence: AT3G23640.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ29185 (Selaginella moellendorffii), 5'ss of exon 8
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
|||| || | |||||| ||| || | || || || ||||| || || || ||||| ||||||||||||||||| ||||| ||||||||||| ||| | ||| | || || |||| | | | | | || ||
AAAGAAAGTCCGTGCATGGTGGAGTAACCTGATAAAAGACTTCGTTTCTAACGGAGTCGATGGCATATGGAATGATATGAACGAGCCCGCTGTTTTCAAGgta--caaatgtatttaaaaaatgagttcaagtttaaaacttaagtaaa---ctaatgcag-------------------------------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|116389361|gb|EG431953.1|EG431953EST: ATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAA GTCGTGACAAAGACGATGCCTGAGAACAATATTCACCATGGAGATGATGAG
genomic: ATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaatttttt ... caatgtccagGTCGTGACAAAGACGATGCCTGAGAACAATATTCACCATGGAGATGATGAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCCAAAGCACGCTCTTGGTGGGCTAATTTGGTTAAGGAATTTGTTTCAAATGGTGTTGATGGTATATGGAATGATATGAATGAGCCAGCTGTTTTCAAAgtaattttttatatattctgcattcactcttttttattttcttggcagaatctttatccaaatttcatatggtcatatttgtcaatgtccag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT