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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag

Basic information

species Arabidopsis thaliana
transcript AT4G38510.4
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 8
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgca-------agtctcgcaatcacactacagacatct-tgaagcaaatt-ttagttccaatgtttttctgaaggtttctcattctgttttccgcacag---
||| || || ||||| ||||||||||| || || ||||| || ||||||||||| || |||||||| || |||||| | || || ||||| || ||  ||| |        | || |  |       ||  ||||   |  | ||  || ||  ||| || |      | |    ||||     |||||| |   ||    
GTTTGCTGCTATGGGAGTGAACATGGAAACAGCTCAATTCTTCAAACGTGATTTTGAAGAGAATGGTTCCATGGAGCGGGTCACCCTTTTTCTGAATCTGgtacctacaaggacttgtgaatttgtaaccaacattcatttatcattttatttcttctaagggcgccataatcaattct-gcaatgttttacatgcatctt

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA10G42940.1 (Glycine max), 5'ss of exon 8
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctc--gcaatcaca--ctacagacatc----ttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag---
 || ||||| ||||| || ||||||||||||||||| ||||| |||||||| || |||||||||||||| |||||||||||||||||||||||||| |||| ||  ||    |||| | |  || |  || ||    ||  | ||    |||  |    | |||   || |||      |    ||   |   | |    
ATTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaaccctttaacaattaaaatctgccaacgtcactattacatcatcaattaactttgttatttgaatgcagggactaaaagtggtgaccaagaaaaggt

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA20G24070.1 (Glycine max), 5'ss of exon 9
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctc--gcaatcaca--ctacagacatc-ttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag------
||| ||||| ||||| || ||||||||||||||||| ||||| || ||||| || |||||||||||||| |||||||||||||||||||||||||| |||| || |||     ||| | |  ||    || || | |   |    |  | |     | |||   || ||       |  | ||       | |       
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAGCGTGACTTTGAGGAGAATGGATCAATGGAGAGAGTGACTCTTTTCCTTAATTTGgtaattctttaaaaattaaaatctgttaacgtcgtcgttacgtcatcaattaatgttatttgaatgcagagactaaaagcggtgacgaagaaaatgttta

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA09G38110.2 (Glycine max), 5'ss of exon 8
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagacatc--ttgaagcaaattt-----tagttccaatgtttttctgaag--gtttctcattctgttttccgcacag--
||| ||||| ||||| || ||||||||||||||||| ||||| |||||||| || ||||||||||| ||||||||||||||||| |||||||||||  ||| |    |   || ||   | || |  |   || |  |  ||||     | |||    ||  || ||||     ||  |  |  | || ||     ||  
GTTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAGAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGgtagtctttagaaccagtatgcaaatgttcttttattcccatttctttgttgtttacttgccttcctgatttccttctttgtaattttatctatgtagtt

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 8
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagaca---tcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag---------
 || ||||| ||||| || ||||||||||||||||| ||||| |||||||| || ||||| ||||| ||||||||||||||||| |||||||||||  ||| |    |   || ||   | || |     | ||    | | || |   |    |  ||  ||  |  |   || || |  |||   |   |         
-TTTGCAGCTATGGGAGTTAACATGGAGACTGCACAGTTTTTCAAACGTGACTTTGAGGAAAATGGCTCGATGGAGAGAGTGACCCTTTTCCTTAATCTGGtagtctttagaaccagtatgcaaatgctcttttattcctatttctttgttgtttacttgccttcatttccttctttgtaattttgtctatgtatttgaga

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 8
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaa-tcacactacagacatcttgaagca-----aattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag------------------------
 || ||||| ||||| || ||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||||||| ||| |  | |   || | |   ||  |  || |   |          | | | ||| ||  |||     | | ||    ||  |    |  | | ||                        
TTTTGCAGCTATGGGAGTAAACATGGAGACTGCACAGTTTTTTAAACGTGATTTCGAGGAAAATGGATCAATGGAGAGAGTGACTCTATTCCTTAACCTGgtatttatattaaattaatatagtggtatttattattgtttgtggtgtaaattctaaattttaaaccaggcttcagaatagttggctttgaatagtttctgatatgctcaagtggacag

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactaca----------gacatcttgaagcaaattttagttccaatgtttttctg----aaggtt---tctcattctgttttccgcacag
 || ||||| ||||| || ||||||||||| ||    || || ||||||||||||||||| || || || |||||||||||||| ||||| || || |||| |  |||| |  | |  || ||           |||     |||  |  || |       ||| || ||     |    |   ||| ||||  ||| ||      
TTTTGCAGCTATGGGAGTTAACATGGAGACAGCTACCTTCTTCAAACGTGATTTCGAGGAAAACGGGTCCATGGAGAGAGTGACACTTTTTCTCAATTTGgta--tctcacttttaatcttcatcttctgtttaacacggcaaagatatcttcaccgtggttgtgttcctagttcagaactagctcttattccttttccctg----

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcg----caatcacactacagacatcttgaagcaaattttagttc-----caatgtttttctgaaggtttctcattctgttttccgcacag--
                 | ||||||||||| ||    || || |||||||||||||| || |||||||| |||||||||||||| ||||| || ||||||| | || ||      |||    ||  |  | |||   |    |||  ||| |     |||  |  | |||   ||          |      | |  |  
-----------------TTAACATGGAGACAGCTACTTTCTTCAAACGTGATTTCGAAGAAAATGGATCTATGGAGAGAGTGACACTTTTTCTCAACTTGgtatgtttcaatcttaatattcctgtatccctctaccacagcattggagtacatactcaacttcgtcctggttgtactctggatggaagcgtggagtgtt

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 5'ss of exon 7
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagacatc-ttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag--------------------------------------------------------------------------------------------------------------
 ||||| || ||||| ||||||||||| |||||    || || ||||| ||||| || || |||||||| |||||||||||||| ||||| || || |||| | ||  |    |||   | |    ||| | ||     |    | ||      | | | || |  ||  ||    |  ||| || |  |                                                                                                              
TTTCGCCGCTATGGGAGTGAACATGGAAACTGCCACTTTCTTCAAACGCGATTTTGAAGAAAATGGATCCATGGAGAGAGTGACACTTTTTCTCAATTTGgtatgta-catcttcagttttcttttatcgtcgattttcaccacatttttggattatatatggaacttcatccagtttcttttcgtaatggaagagtcgtctgttttgagacttcacaaagtcaattttcctccagtccttgcgtttttttcctggattaagttctggaattttattttaggatcgtcttgggctttcag

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ11911 (Selaginella moellendorffii), 5'ss of exon 7
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag
 || ||||| |||||||||||||||||||||||||| ||||| ||| | ||||| ||||| |||||||||||||| ||||| ||  | ||| | ||| ||| | ||   | | | ||| | |  |    ||        ||     ||||  || ||||  |  |                        
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGGGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgtacgttatggattgacaatgccaatgcgttt-------ttactcctccatcgtgtttcgtacag------------------------

upper sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ13375 (Selaginella moellendorffii), 5'ss of exon 7
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag
 || ||||| |||||||||||||||||||||||||| ||||| ||| | ||||| ||||| |||||||||||||| ||||| ||  | ||| | ||| ||| | ||   | | | ||| | |  |    ||        ||     ||||  ||  |||  |  |                        
CTTTGCAGCTATGGGTGTGAACATGGAGACTGCACAGTTTTTCAAAAGAGATTTTGAGGAAAATGGATCGATGGAAAGAGTCACATTGTTCTTAAACCTGgtacgttatggattgacaatgccaatgcgttt-------ttactcctccatcgtgcttcgtacag------------------------

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|164097611|gb|ES030150.1|ES030150
EST:     GTGACTCTTTTCCTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
genomic: GTGACTCTTTTCCTTAACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
EST: gi|86066802|gb|DR362559.1|DR362559
EST:     ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
genomic: ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
EST: gi|163992106|gb|ES203115.1|ES203115
EST:     TTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCA
genomic: TTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTT-AACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCA
EST: gi|116450411|gb|EG493003.1|EG493003
EST:     ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTG                         GCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA
genomic: ATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcg ... ttccgcacagGCAAACGACCCCACTATTGAGCGTATCATCACTCCTCGTATCGCACTTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGCAGCAATGGGTGTGAACATGGAGACTGCACAATTTTTTAAACGTGATTTCGAGGAGAATGGATCGATGGAGAGAGTGACTCTTTTCCTTAACTTGgcaagtctcgcaatcacactacagacatcttgaagcaaattttagttccaatgtttttctgaaggtttctcattctgttttccgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA