Sequence
atgc intronic sequence ATGC exonic sequenceAATGTAATTCATGGTGACATCAAACCTGACAATTTACTGGTTACTAGTACCGGGAGAGTGAAAATAGGAGATTTCAGTGTCAGCCAAGTATTCAAAgtactgatgataccatttcttttcttctttttcttctccgttaatctctgtaatgtgtaatttgatctgctaaaacatgatacatttgatgaag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G45240.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G45240.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os03g50330.1 (Oryza sativa), 5'ss of exon 8
AATGTAATTCATGGTGACATCAAACCTGACAATTTACTGGTTACTAGTACCGGGAGAGTGAAAATAGGAGATTTCAGTGTCAGCCAAGTATTCAAAgtactgatgataccatttcttttcttctttttcttctccgttaatctctgtaatgt-gtaatttgatctgctaaaacatga-tacatttgatgaag-----
||| | ||||||||||| |||||||| |||||||| |||| || || || || || ||||| ||||| ||||||||||| || || | || | || | || | | | ||| || | | | | | | ||| | | | ||| | ||| | || |||
AATATTATTCATGGTGATATCAAACCAGACAATTTGTTGGTCACAAGCACTGGCAGTGTGAAGATAGGGGATTTCAGTGTTAGTCAGATTTTTGAGgtgg-gcctttatcctctaacctctgtattgtagtaatgaatgctattttccttgtcatggcataaagggctttcagttgaatggatccccagaaaattgt
upper sequence: AT3G45240.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G133854_T01 (Zea mays), 5'ss of exon 7
AATGTAATTCATGGTGACATCAAACCTGACAATTTACTGGTTACTAGTACCGGGAGAGTGAAAATAGGAGATTTCAGTGTCAGCCAAGTATTCAAAgta--ctgatgataccatttcttttcttctttttcttctccgttaatctctgtaatgtgtaatttgatctgctaaaacatgatacatttgatgaag-----
||||| ||||||||||| ||||| || |||||| | ||||||| |||||||| | ||||| || || ||||||||||| ||||| || || | || | | | || | || | |||| | | || | |||| || | ||| || ||| | || || |||| ||
AATGTTATTCATGGTGATATCAAGCCAGACAATCTCTTGGTTACCAGTACCGGCAACGTGAAGATCGGGGATTTCAGTGTTAGCCAGGTTTTTGAGgtggtttctttagtcctgtaacttgtgtattttattgattttttcttgtctggaa-acattgttttttcagctgattgatcccacccttgaaagagataaa
upper sequence: AT3G45240.3 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G057084_T01 (Zea mays), 5'ss of exon 8
AATGTAATTCATGGTGACATCAAACCTGACAATTTACTGGTTACTAGTACCGGGAGAGTGAAAATAGGAGATTTCAGTGTCAGCCAAGTATTCAAAgtactgatgataccatttcttttcttct--ttttcttctccgttaatctctgtaatgtgtaatttgatctgctaaaacatg-atacatttgatgaag---
||||| ||||||||||| |||||||| |||||| | ||||||| ||| |||| | ||||| || || ||||||||||| ||||| || || | || | ||| | || | | ||| | || | ||| ||| | ||| | | | | ||| || || |||
AATGTTATTCATGGTGATATCAAACCAGACAATCTCTTGGTTACCAGTGCCGGCAATGTGAAGATTGGGGATTTCAGTGTTAGCCAGGTTTTTGAGgtggtttctgtactcctgtaactcatataatttagtgtgtttttttcttttgttatggaaatattgttttccagtcaaatggatgcacccatgaaagggaMapped 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|124717742|gb|EH809144.1|EH809144EST: GTACCGGGAGAGTGAAAATAGGAGATTTCAGTGTCAGCCAAGTATTCAAA GATGATGATGATCAACTCCGTAGATCACCCGG
genomic: GTACCGGGAGAGTGAAAATAGGAGATTTCAGTGTCAGCCAAGTATTCAAAgtactgatga ... tttgatgaagGATGATGATGATCAACTCCGTAGATCACCCGG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AATGTAATTCATGGTGACATCAAACCTGACAATTTACTGGTTACTAGTACCGGGAGAGTGAAAATAGGAGATTTCAGTGTCAGCCAAGTATTCAAAgtactgatgataccatttcttttcttctttttcttctccgttaatctctgtaatgtgtaatttgatctgctaaaacatgatacatttgatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT