Sequence
atgc intronic sequence ATGC exonic sequenceCAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGGTACATATCGTTGGATGGCTCCCGAGgtacttaatggaatcttgcattttctgtgttctgcatttttcttttgcttctaagaacttgcttaatcacaaattacggttaaacag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40540.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g38080.1 (Oryza sativa), 5'ss of exon 5
CAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGGTACATATCGTTGGATGGCTCCCGAGgtacttaatggaatcttgcattttctgtgt-tctgcatttttcttttgcttctaagaacttgcttaatcacaaattacggttaaacag
| || || || || | || |||||||||| |||||||| ||||||| ||||||||||| ||||| || || ||||| |||||||||||||| ||||| | | |||| || | | | || || ||||||| || | | | ||||| |||| || || | |
GAGAACAGTCAAGCTTGTTGACCTTGGTTTAGCAAGAGAAGAGACATTAACAGAGATGATGACTGCAGAGACAGGAACATACCGTTGGATGGCTCCAGAGgtttctgtta-----ctgcagttcatatttgtcaatataattctttt--ttgtcaatatttgct-aatcctgaaatatatccacag--
upper sequence: AT5G40540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G165231_T01 (Zea mays), 5'ss of exon 4
CAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGGTACATATCGTTGGATGGCTCCCGAGgtacttaatggaatcttgcattttctgtgttctgcatttttcttttgcttctaagaacttgcttaatcacaaattacggttaaacag
| || || ||||| | ||| ||||||| ||||| ||||| || |||| ||||||||||| || || || || ||||| |||||||||||||| ||||| || || | | | ||||| || ||||| | || ||| || | | | ||| | | | | |||||||
GAGAACAGTAAAACTTGTTGATCTTGGTTTGGCTAGGGAAGAGACACTAACGGAGATGATGACTGCTGAGACAGGAACATACCGTTGGATGGCTCCAGAGgtttctactgcatccat--atttttagt-ttctgagtccttaattttctgt--attattaatgtaacctgggaattc---taaacag
upper sequence: AT5G40540.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv14s0066g00370.t01 (Vitis vinifera), 5'ss of exon 4
CAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGGTACATATCGTTGGATGGCTCCCGAGgtacttaatggaatcttgcattttctgtgttctgcatttttcttttgcttctaa--gaacttgcttaatcacaaattacggttaaacag-----------------
||| ||||| ||||| || |||||||| ||||| |||||||| |||||||| ||||||||||| || |||||||| || ||||||||||||||||| ||||||||||| | ||| |||| | | ||| ||| ||||| | | | | | | || ||| | | ||
CAAAACTGTCAAACTTGCGGATTTTGGCTTAGCCAGAGAAGAGTCATTAACAGAGATGATGACTGCCGAAACTGGAACGTATCGTTGGATGGCTCCAGAGgtacttaacact-taatgc-ttttatttattcattcatttatttttgttggtgaatggggaaggggactccagaatgctgaccattcacctttcactttgttgtagMapped 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|116473897|gb|EG516489.1|EG516489EST: CCGAGATGATGACCACAGAAACTGGTACATATCGTTGGATGGCTCCCGAG CTTTACAGTACGGTCACGTTGAGGCATGGTGAGAAAAAACACTATAACCAT
genomic: CCGAGATGATGACCGCAGAAACTGGTACATATCGTTGGATGGCTCCCGAGgtacttaatg ... ggttaaacagCTTTACAGTACGGTCACGTTGAGGCATGGTGAGAAAAAACACTATAACCAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAAGACTGTTAAACTAGCAGATTTTGGTTTAGCTAGAGAAGAATCATTAACCGAGATGATGACCGCAGAAACTGGTACATATCGTTGGATGGCTCCCGAGgtacttaatggaatcttgcattttctgtgttctgcatttttcttttgcttctaagaacttgcttaatcacaaattacggttaaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG