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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaacttcttaccatgatatatcgaacatgaatttgatctaatccaccgtagaattctttgttcctaattttcatttttctcttcag

Basic information

species Arabidopsis thaliana
transcript AT5G23300.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os04g57950.1 (Oryza sativa), 5'ss of exon 4
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaa----cttcttaccatgatatatcgaacatgaatttgat-ctaatccaccgtagaattctttgttcctaattttcattt-ttctcttcag-----
 ||  | || ||||| ||||| ||||||||||  || || |||||| |||||||||| || |||||||||||||   |||| || ||||||||||||||||||   |    |||||   || || | | |  ||||| || || | ||| |  | | ||    |     ||  | |  || |||  ||| |   ||     
AATCTTGGGAGTCAATCTTGGGAAGAACAAGATCAGCGAAGATGCTACTGCTGACTACGTGCAAGGAGTTCATACACTATCACAATATGCTGATTACTTGgtattcatcctcttctcttcaagaaa-acctcacatggatgtgtttctacttgaacctaagcataccatttgttcacattgattggttcacactagttttg

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G043776_T01 (Zea mays), 5'ss of exon 4
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaacttcttac-catgata--tatcgaacatgaatttgatctaatccaccgtagaattctttgttcct--aattttcatttttctcttcag------
 ||  | || ||||| ||||| ||||||||||| ||||| |||||||||||||| ||||| ||||| |||||||  || || || |||||||||||||||||||       || | ||   ||  | |  |  || | |||| | |  |||    |   |||   ||||  |  ||     | |||    || |       
AATCTTGGGAGTCAATCTTGGCAAGAACAAGACTAGTGAAGATGCTGCTGCTGATTATGTGCAAGGGGTTCATACATTGTCACAATATGCTGATTACTTGgtacctgtcctttgcacacagtaattttacactataattttggtatt-tccggtttcatattagctgtttttagaaccagaaatttcgcatttatttattt

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G43220.1 (Glycine max), 5'ss of exon 4
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgta-caaacttcttaccatga------tatatcgaacatgaatttgatctaatccaccgtagaattctttgttcctaattttcatttttctcttcag---
 |||||||| ||||| ||||||||||||||||| ||||| |||||||| || || ||||| |||||||||||||  || ||||| |||||||||||| |||||   |   | ||   |||       | ||| ||| | |||    |    |  || | | | || || |        ||   ||   |   | |||   
CATTCTTGGTGTCAATCTTGGAAAGAACAAGACAAGTGAAGATGCTGCAGCAGATTATGTTCAAGGAGTTCATACATTGTCCCAATATGCTGATTACCTGgtaattagtcttttcttatgtatgccttttatagaaaaagaagggaaagatagacaaccttgtatactgtaacttatcttggtatgactgagtgcagatt

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA20G23670.1 (Glycine max), 5'ss of exon 4
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaacttcttaccatgatatatcgaacatgaatttgatctaatccaccgtagaattctttgttcc-taattt-tcatttttctcttcag---------
 || ||||| ||||| ||||||||||||||||| ||||| ||||||||  | || ||||| |||||||||||||  || ||||| |||||||||||||||||| | | |  || |    || |  |    ||  |   ||    |   |  | | ||   | | | |  |||||| || |  |     | ||         
CATCCTTGGTGTCAATCTTGGAAAGAACAAGACAAGTGAAGATGCTGCGTCAGATTATGTTCAAGGAGTTCATACATTGTCCCAATATGCTGATTACTTGgtaaatagtcttttcttatatgtgccttttatagaaaagaaaggaaagatag-acaaccttatatactgtaatttatcctggtatgactgagtgcagatta

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv10s0042g00140.t01 (Vitis vinifera), 5'ss of exon 4
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaacttcttaccatgatatatcgaacatgaat-ttgatct---aatccaccgtagaattctttgttcctaattttcatttttct--cttcag------
 |||||||||||||||||||||||||| ||||| ||||| ||||||||||| || ||||| ||||| ||||||   ||||||||||||||||||||||||||| ||| || ||  | |  |  |    || | ||| ||  |||    ||   | | ||    |   | |  |    |||| || | |   ||  |      
CATTCTTGGGGTCAACCTTGGAAAGAATAAGACAAGTGAAGATGCTGCTGCAGATTATGTACAAGGGGTTCATTCATTATCCCAGTATGCTGATTACTTGgtagaaatttttt--ctttcttcagtacactttaatgttagtcttaggatttcctgcaggcaacaaagatagtggacttcagttctttgattttggacatgg

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S29_152V6.1 (Physcomitrella patens), 5'ss of exon 5
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaacttcttaccatgatatatcgaacatgaatttgatctaatccaccgtagaattctttgttcctaattttcatttttctcttcag-------------------------------------------------------------------------------------------------------------------
 ||  | || || || ||||||||||| ||||||||||| ||||| || ||||| ||||| ||||| || |||| ||| || || |||||||||||| |||||   |  | ||  |  |  |  |       ||  ||||| |  |    || | |  |||  |  | |   |||  || ||| |   ||                                                                                                                   
GATATTAGGTGTAAATCTTGGAAAGAATAAGACGAGTGAAGATGCCGCAGCTGATTATGTACAAGGCGTGCATACCTTGTCTCAATATGCTGATTACCTGgta---agctattgtcgagccac-taacctgcgatgttgattttttatgtcg-atacatctcagagcttggatttttttattccccgtaggtgcagtaccctggtacgttacgtataaggtaagttgcttgtatccagaataatgagtacaggtcattacaaatcaagccattgatggtacagacgtggtggaaattttttgcag

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S291_29V6.1 (Physcomitrella patens), 5'ss of exon 4
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaacttctt--accatga-tatatcgaacatgaatttgatctaatccaccgtagaattctttgttcctaattttcatttttctcttcag-------------------------------------------------------------------------------------------
 ||  | || || || || |||||||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||||| ||| || || ||||||||||| ||||||  |   |  |  | ||  |   | ||      || ||| | || | | | | |   |     ||      ||| | ||  || | ||  |                                                                                           
GATAGTAGGAGTAAATCTGGGAAAGAATAAGACCAGTGAAGATGCTGCAGCTGATTATGTACAAGGGGTTCATACCTTGTCACAATATGCTGATTATTTGgtaagattatgctgaatcacaagcctgtcatgttggattttcaccttaacaaacctctgagaagctgcattctattataatagttttattgtgtatgacaagatgaatattttaagaagaaagagttcaggtcatcacaaatttaagatactgattgtgcatatcctgtggagattgcttgcag

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|116483520|gb|EG526112.1|EG526112
EST:     CTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTG                         GTGATCAATGTTTCATCACCCAATACTGCAGGACTGCGCATGCTTCAAGGA
genomic: CTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaactt ... ttctcttcagGTGATCAATGTTTCATCACCCAATACTGCAGGACTGCGCATGCTTCAAGGA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTCTTGGGGTCAACCTTGGAAAGAACAAGACGAGTGAGGATGCTGCTGCTGACTATGTCCAAGGAGTTCATAACTTATCCCAGTATGCTGATTACTTGgtacaaacttcttaccatgatatatcgaacatgaatttgatctaatccaccgtagaattctttgttcctaattttcatttttctcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT