Sequence
atgc intronic sequence ATGC exonic sequenceTTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G08530.1 |
intron # | 21 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag---------
|||| ||||| |||||||| || | |||||||| ||||| ||||| || || |||||||||||||||||||| || || |||||||| || ||||||||| || | | |||| || ||||| ||| | | | | | | ||||| ||| || ||||| |
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgta-gttgtgtgtttcgact-ctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 21
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag---
|||||| ||||| ||||||||||| | ||||| || ||||| || || || || ||||||||||||||| |||| |||||||||||||| || |||||||||||| | | | || | | | | | | | ||||| | || ||| || | || | || || |
TTTGATTAATGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagccttgcttatctcatgagtgcta---tctactctttttctctgcc-tatgtaaaacttcgtgcctttctatacag
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag---
|||||| || || ||||||||||| | ||||| || ||||| || || || || ||||||||||||||| |||| |||||||||||||| || |||||||||||| | || | || | ||| ||| | | | ||||| | || ||| || | |||| || || |
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgcttatctc--atg-attgctatctactctttttctctgcc-tatctaaaactttgtgcctttctatacag
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 20
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatattta-tacgtttgattctgtcaaag--------------------
| |||| ||||| ||||| || || | ||||| || ||||| || || || || |||||||||||||||||||||||||||||||| || || |||||||||| | || | || | | | ||| || | | | ||| | ||| || | | || | ||| |
TCTGATTAATGTTTGTGACCGATTTGGATTTGTTCCGGATCTAACACACTATCTATACACAAACAACATGCTTCGTTACATTGAAGGTTATGTTCAGAAGgtattatagtttgcattaataatgctgtaaccttgctttttacatgaatactatctagtatctactttctctgccccactcataactttgtgccttgttttatag
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 20
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtat-aaggtttcc--tgggactacttttaatgcgtt--------ggagttcagtttttttttatgaaatatttata-cgtt-tgattctgtcaaag
| | || ||||| ||||| || || | ||||| || ||||| || || || || ||||||| |||||||||||||||||||||||| || || |||||||||| | |||| | | | | || | | | | | | | ||| | || | | ||| | || || | | | ||
TCTAATTAATGTTTGTGACCGGTTTGGATTTGTTCCGGATCTAACACACTATCTATACACAAGCAACATGCTTCGTTACATTGAAGGTTATGTTCAGAAGgtattatagtttgcattaataatgctgtaatcttgcttattacacaaatactatctactttctctgccccactcataacattgtgccttctttatag
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 21
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtt-tcctgggact-----acttttaatgcgttggagttcagtttttttttatg-aaatatttatacgtttgattctgtcaaag----------------------------------------------
|||| ||||| ||||| ||||| | ||||| || ||||| || |||||||| ||||| |||||||||||||| || |||||||| || || || ||||| | || | | || | | | | ||| || | | | ||| | | || || || | | | | | ||
GCTGATTAATGTGTGTGACCGTTTTGGTTTTGTCCCAGATCTCACACATTACCTATACACGAACAACATGCTTCGATATATTGAAGGTTATGTTCAAAAGgtgtgagttccttctagaattctagaattttggatcccctttgggtcatgatgaactcctgtggatgcttcaatgccctaattaattttagtcttcaattatttgattaaattaattgcttttgcttctcttgatag
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 21
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgta---taaggtt--------------tcctgggactactttta--atgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag------------------
| | || ||||| || ||||| |||||||||| ||||||||||||| ||| || ||||| |||||||| || |||||||| || |||||||||||| | || || || | || | | | || ||| || | || | | | || ||| | | | || || |||||
TCTCATCAATGTTTGCGATCGACATGGCTTTGTGCCAGATCTTACTCATTTCCTTTATGTCAACAATATGCTTCGATATATTGAAGGATATGTGCAGAAGgtaatttgagattcaatgatacatggttcgtaagaattcctgtacaatgagtaaaaattgattctccttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcag
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 21
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag
| | || || || || ||| | ||| | | || || ||| | || || ||| | || | |||||||||||||| || |||||||||||||| || |||||| || ||| | | | ||| ||| | | | ||||| ||||| || |
TCTCATCAACGTGTGCGATAGATTCGGTTACGTTCCGGATTTGACACACTACTTGTATTCGAACAACATGCTTCGGTATATTGAAGGCTACGTCCAAAAGgtac--ggattc-----aatgcatttgttgctctataatc--gtttt-------gaaattttcag-------------------
upper sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 21
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag
| | || || || |||||| | ||| | | || |||||| | || || ||| | || | |||||||||||||| || |||||||||||||| || |||||| || ||| | | | ||| ||| | | | ||||| ||||| || |
TCTCATCAACGTGTGTGATAGATTCGGTTACGTTCCTGATTTGACACACTACTTGTATTCGAACAACATGCTTCGGTATATTGAAGGCTACGTCCAAAAGgtac--ggattc-----aatgcatttgttgctctataatc--gtttt-------gaaattttcag-------------------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|124936463|gb|EL013354.1|EL013354EST: ACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAG GTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGA
genomic: ACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtt ... tctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG