Sequence
atgc intronic sequence ATGC exonic sequenceATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttgttcacttttaactcaagatattttgttcaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G03540.3 |
intron # | 6 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os11g05880.1 (Oryza sativa), 5'ss of exon 5
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttgttcacttttaactcaagatattttgttcaacag--
||| ||||| || || ||||| ||||||||||| |||| |||||||||||||| ||||||||| ||||||||||| ||||||||||| ||||| ||||| || | | ||| | || || | | || || || | || || | | || || | | |||
ATTAGGAGTAGAGAAGCTTAGTAAAGAGGATGTACAGAAGATGCAGTGGGAAGCTTTGGAGGCTAAAATTGGAAACTGGATCCATTTTATGCGAATTGCGgtggggattctt-ctgagaataggtccatattgtgtatattcag---accttaagactcatattttgcttacgacacag
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 5
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgt-tttgtt--cacttttaactcaagatattttgttcaacag
||||| ||||||||||| |||||||| || || |||| |||| |||||| |||||||| | ||||| || |||||||| || |||||||| ||||||||||| | | | | | | |||||| | || | ||| ||| || | | |
CTTGGGTGTTGAAAAACTGAGCAAAGATGAAGTGCAGAAAATGCCATGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCACTTCATGCGAATTGCTgtaaggatttttctcttatctactgtatggtgcaacatgcctctggtgacaccttttgctttaaacag------------
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GRMZM2G046590_T01 (Zea mays), 5'ss of exon 5
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttg--ttcacttttaactcaagatattttgttcaacag--
||||| |||||||||||||||||||| || || |||| |||| ||||||| |||||||| | ||||| || |||||||| ||||||||||| ||||||||||| | | | | | | | ||| | | | || | || | || | | |
CTTGGGCGTTGAAAAACTTAGCAAAGATGAAGTGCAGAAAATGCCGTGGGAAATTTTGGAGTCTAAAATAGGGAATTGGATTCATTTCATGCGAATTGCTgtaagtaatttccctccctccctcaggtcttctgttatggtatagcattgctctggtgacatttgcctctgcttgagacag
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G17500.1 (Glycine max), 5'ss of exon 2
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttgttcacttttaactcaagatattttgttcaacag
| |||||||||||||| |||||||| ||||| || | | | || ||||| |||||||| |||||||||||||| ||||| ||||||||||| |||||||||||| | || || || || | | ||| | | || | || | ||||| | | | | || |||||
GCTTGGAGTTGAAAAACTAAGCAAAGATGATGTTCAAAAGCTACAATGGGAGGTTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATTGCTgtaagaccact-gtcaaatttgttcacatattttatct-ttatattttcatttaaatatgcaattgtacttgaacag
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 5
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttgttcacttttaactcaagatattttgttc-aacag
| || ||||| ||||| |||||||| ||||| || | | | || ||||| |||||||| |||||||||||||| ||||| ||||||||||| |||||||||||| | || || | || | | ||| || |||| || | | || | | |||| | | |||||
GCTTGGTGTTGAGAAACTCAGCAAAGATGATGTTCAAAAGCTACAATGGGAGGTTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATTGCTgtaagaccact-gtcgaatttgtttacatattttttattttttttttcatgtaaat--atgctattgtacttgaacag
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 5
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaaga--actctag--ttaaggatggaaataactttaacatgttttgttcacttttaac--tcaagatattttgttcaacag------
| | ||||| || ||||| | |||||| ||||| || | | |||||||||| ||||||| |||||||||||||| ||||| ||||||||||| || || |||||| | | ||| || | || | ||| | || ||| || | | | |||| | || |||
ACTTGGAGTGGAGAAACTCAACAAAGATGATGTTCAAAAGCTGCAGTGGGAGATTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATAGCAgtaagatgattgtaggattggtgctgtgttttttttttgtcttcattattcttttaatatctttcaaatatgtaattatacatgaacag
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 5
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaaga--actctagtta-aggatggaaataactttaacatgttttgttcacttttaac----tcaagatattttgttcaacag------
| | ||||| || ||||| | |||||| ||||| || | | |||||||||| ||||||| |||||||||||||| ||||| ||||||||||| || || |||||| | | || ||||| | || || || |||||| | | |||| | || |||
ACTTGGAGTGGAGAAACTCAACAAAGATGATGTTCAAAAGCTGCAGTGGGAGATTTTGGAAGCCAAAATTGGAAACTGGATTCATTTCATGCGTATAGCAgtaagatgaagatgattgtaggattggtgctgtgttttttgtcttcattattttttaatatctttcaaatatgtaattatacacgaacag
upper sequence: AT5G03540.3 (Arabidopsis thaliana), 5'ss of exon 6
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 5
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttgttcacttttaactcaagatattttgttcaacag----------------------
|||||| || ||||| ||||||||||| ||||| |||| |||||| ||||| ||||||||||| || ||||| |||||||| ||||||||||| ||||||||||||| || || || || || | || || | | | | |||| | | ||
ATTGGGTGTGGAAAAGCTTAGCAAAGATGATGTTCAGAAGATGCAATGGGAGGTTTTGGAGGCTAAGATTGGGAATTGGATTCATTTCATGCGGATTGCTgtaagaatatatgtcaaatttgcggg-aatttaggtgtattaaatttgcatgcatttatgtatatctgctcttccaattctgttattttacataaacagMapped 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|164024323|gb|ES054114.1|ES054114EST: GCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCT GTTAAATTACTCTTTGCTGGTGAAAGACAAGTATATGACCAGATATTCCGA
genomic: GCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactc ... tgttcaacagGTTAAATTACTCTTTGCTGGAGAAAGACAAGTATGTGACCAGATATTCCGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTGGGAGTTGAAAAACTTAGCAAAGAGGATGTCCAGAGGATGCAGTGGGAAGTTTTGGAGGCCAAAATTGGAAATTGGATCCATTTCATGCGCATTGCTgtaagaactctagttaaggatggaaataactttaacatgttttgttcacttttaactcaagatattttgttcaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG