Sequence
atgc intronic sequence ATGC exonic sequencegtaagaactcaacctcactggattgtaacatgttgatttgatataatcctcggataatagatagattggcctttgaaactctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G14940.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------------------------gtaagaactcaacctcactggattgt--aacatgtt-gatttgatataatcctcggat-----aatagatagattggcc--tttgaaactctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
| | || | | ||| || |||||| ||||| | || ||| || || | | ||| || || || |||||||||| || || |||| |||||||| ||||||| | ||||| || |||||||||||||| ||||| |||||||| || || |||||||||||||
gtaagataatcaagttaatcactgactcatttatagtcttgattttttttttcaaattgtatgtgccttttcgattatttatagaaattataaattactttcagcatgatgctcaacatgccagattttgtgctccaactaaatttattaatgcattaataaggtgaatcagaacatgttcttatttttcagATTCAAGCAGCCTTTAGAACTGATGAGATCCGAAGAACCCAGCCAACTCCTCAAGATGAAATGAGGGCTGGTATGAGTTACTTTCATGAGACAATCTGGA
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------gtaagaactcaacctcactgg--attgtaacatgtt----gatttgatataatcctcggataa---tagatagattggcctttgaaactctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
| | || | || | || ||| |||| |||||| ||| | ||| || || | | | | | | || |||| |||| ||||| || || |||||||||| ||| | || ||||||| || ||||| ||||||||| | ||||||||||||||||| || |||||||| ||||
gtgatttcctttttgtaggagcttggattatgagtggcacaagaccactatagtgattatttcaacaatcagcaagatttgtcatacatcaaaaatatatttatatgattctaattccttatattttttcttatgttcagATCCAAGCCGCCTTTAGAACAGATGAAATTCGGCGAGCACCTCCTACACCACAGGATGAAATGCGTGCTGGAATGAGTTATTTTCATGAGACAATATGGA
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 3
---------gtaagaactcaacctcact---ggattgtaacatgttgattt-gatataatcctcggataatagatagattggcctt----tgaaact--ctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
| || | | | ||| | | || || ||| || | | | || ||| ||| | | || | | | || ||||||| |||||||| || |||| |||||||| ||||||||| || || || |||||||||||| | ||||| ||||| || ||||| || ||||| ||||
gtacttgttgcaaacatt-atgttcatttacaaaatgctttgcattattttcagcatgaggtcagaaagatccataatccattcttatgcttcacctgacatcctattattttagATCCAAGCTGCCTTTAGAACCGATGAGATCCGAAGAACACAGCCCACTCCCCAAGATGAAATGCGTGCTGGCATGAGCTACTTCCATGAAACAATATGGA
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 3
gtaagaact-caacctcactggattg--taacatgttgatttgatataatcctcgga---taatagatagattggcctttgaaa----ctctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
||| | ||| || | | ||| ||| || | | | | || || |||| || || |||| ||||| || ||| | |||| |||||||| || |||| |||||||| ||||||||| || || || |||||||||||| | ||||| ||||| || |||||||| ||||| ||||
gtacttctttcaatctaattttattacctaaaattctttgaagcttgagaccaaagagattaattcttaatttcttacctgaatacctctctctttctttttcaagATCCAAGCTGCCTTTAGAACTGATGAGATCCGAAGAACACAGCCCACTCCCCAAGATGAAATGCGTGCTGGTATGAGCTACTTCCACGAAACAATTTGGA
upper sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 3'ss of exon 3
---------gtaagaactcaacctcactggattgtaacatgttgatttgatataatcctcggataatagatagattggcctttgaaactctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
| | ||| | | || ||| || | | ||| | | | | ||| || || ||| | ||| ||||||||||| || || || || ||||| ||| | ||||| ||||||| ||||||||||| ||||| || |||||||| ||||||||||||||||||||||
tgctttgagatgggtactggatcct--tgaattagaataaggaattttttatttttatttttgctttcctcagacctaccattt---ctccttctccctgtgtagATTCAAGCCGCCTTTCGTACGGATGAAATTCGGAGAACTGCTCCAACTCCACAAGATGAGATGAGGGCAGGAATGAGCTATTTCCACGAGACAATCTGGAMapped 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|86073317|gb|DR369074.1|DR369074EST: ACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAG ATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCA
genomic: ACATTACTCCTGATGACAAGCAGGAGCTAGATGAGTCTCTGCAAAGAGAGgtaagaactc ... ttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tataatcctcggataatagatagattggcctttgaaactctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
ctctccttttttgttt CT-rich tract
ataatagatagatt TA-rich tract
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaactcaacctcactggattgtaacatgttgatttgatataatcctcggataatagatagattggcctttgaaactctccttttttgtttagATTCAAGCTGCATTCCGAACAGATGAGATTAGAAGAACACCTCCAACCCCACAAGATGAAATGAGAGCTGGAATGAGTTATTTCCACGAGACAATCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA