Sequence
atgc intronic sequence ATGC exonic sequenceTCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagagatctaagttatatctctatttaaaagtcttgtctttgattatatagaattcaatatggactattctattgtttatgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21520.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G171354_T04 (Zea mays), 5'ss of exon 1
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagagatctaagttatatctctatttaaaagtcttgtctttgattatatagaattcaatatggactattctattgtttatgtag
||| |||||||||||||| ||||||| || || || || ||||||| ||||||||||| ||| ||||||||| || || || | || || || |||||| | || || | | | | || | ||||| | || | | | | |||||| ||||| |
TCTATACCAAATGTTTATTGTCAATGCTGGTCCGGGTTTCCGGCTACTATGGAACACTGTGAAGTCCTTTCTTGATCCCAAAACTACCGCCAAGATACATgtaagtttccactgaggcacaa----gcgacagaacttttttcttgataacattgcttaatgtctaaggtattcttatgtttttag--
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA04G01220.1 (Glycine max), 5'ss of exon 6
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagagatctaagttatatctctatttaaaagtcttgtctttgattatatagaattcaatatggactattctattgtttatgtag-------------
||| ||||||||||||||| ||||| ||||||||||||||||| | ||||||||||||||| ||||| || || || ||| || |||| ||||||||||| | | | | |||||||| ||| | |||| | || | | ||| | || | || | | |
TCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAACACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTCATgtatgtataaataccctcttctagctatttaatgatctgtttaatgatggtttaagact--gctgaaactgcttgat-gcttctttggaaacattactcag
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA06G01260.1 (Glycine max), 5'ss of exon 6
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagagatctaagttatatct-ctatttaaaagtcttgtctttgattatatagaattcaatatggactattctattgtttatgtag-------------
||| ||||||||||||||| ||||| ||||||||||||||||| | |||| |||||||||| ||||| || || || ||| || |||| ||||||||||| | || | | | |||||||| ||| | |||| ||||| | | | || | | || || | | |
TCTTTGCCAAATGTTTATTATAAATGCTGGGCCTGGATTTAGGCTGTTGTGGAGCACTGTCAAGTCTTTTCTCGATCCCAAAACAACTTCTAAGATTCATgtatgtaaaatatgccctcttctagctatttaatgatctgtttaatgatgatataagactga---tgaaactgcttgatgcttctttggatacattcctcag
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA12G04460.1 (Glycine max), 5'ss of exon 6
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatg-agagat-ctaagttatatctctatttaaaagtcttgtctt--tgattatatagaattcaatatggacta-ttctattgtttatgtag-------
|||| |||||||||||| || ||||| || |||||||||||| | || ||||||||||||||| || ||||| || |||||| || | || ||||||||||| ||| || ||| || || || ||| |||| || | || | ||| | | || | | | | | | | ||
TCTCTGCCAAATGTTTATCATAAATGCTGGCCCTGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAGACAACTTCAAAGATTCATgtatgtagaaatgctatattgtagct--gcctaaggctcttttcatgatggct-tatggctgctgacattgcttggtgcctctatggaaatattacttag
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA11G12260.1 (Glycine max), 5'ss of exon 6
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatg-agagat-ctaagttatatctctatttaaaagtcttgtctttgattatatagaatt-----caatatggactattctattgtttatgtag-----
|||| |||||||||||| || ||||| || || ||||||||| | || ||||||||||||||| || ||||| || || ||| || | || ||||||||||| | | || ||| || || || || | | | | |||| | || | |||| | ||| || | |
TCTCTGCCAAATGTTTATCATAAATGCTGGACCGGGATTTAGGTTGCTATGGAACACTGTCAAGTCTTTCCTTGATCCCAAAACAACTTCAAAGATTCATgtatgtaaaaatgctatattgtagctgcgtt---aggctcttttcatgatggtttatggctgctgacaatgcttggtgcctctttggaaatattgcttag
upper sequence: AT2G21520.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 7
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagagatctaagttatatctctatttaaaagtcttgtctt-tgattatatagaa--ttcaatatggactattctattgtttatgtag--------------------
|||| ||||||||||||||||||||| || ||||| |||||||| |||||||||||||| |||| ||||| || || || ||| || | || |||||||| | || | | ||| | |||||| | |||| | | | | |||| ||||| || || | | | | | | | |
TCTCTGCCAAATGTTTATTATCAATGCTGGTCCTGGCTTTAGGCTGCTCTGGAACACTGTAAAGACTTTTCTAGATCCCAAAACAACTTCCAAGATTCATgtgcgtgaaa---atgtttttcttctatt----attcttacttcataaattcgtagagccttcaaaatatgctgtataactttgtctctggggtttggaatttctcctcagMapped 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|86064746|gb|DR360503.1|DR360503EST: GGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCAT GTACTCGGATACAAGTATCTAAGCAAATTGCTTGAAGGCATTGATGTCAA
genomic: GGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagaga ... gtttatgtagGTACTCGGATACAAGTATCTAAGCAAATTGCTTGAAGTCATTGATGTCAA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TCTCCACCAAATGTTTATTATCAATGCAGGGCCTGGATTTAGGCTACTCTGGAACACTGTCAAGAGCTTTCTTGACCCTAAGACATCTGCTAAAATTCATgtatgagagatctaagttatatctctatttaaaagtcttgtctttgattatatagaattcaatatggactattctattgtttatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT