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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaatacccttttctagtgttttactgatattcaaactgcaagtaaataactttttgactttcatcattgttcag

Basic information

species Arabidopsis thaliana
transcript AT3G27090.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 2
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatt--tcccaatacccttttctagtgttttactgatattcaaactgcaa-gtaaataactttttg--actttcatcattgttcag----------------------------------------------
||  |    ||||  || || ||||||||||| || ||||| || |||||||||||||||||||| || |||||||||||| | ||  | || || |||||||  |  ||| | |  |||| |||  ||  | |    |   || | ||    |  ||||| ||  ||   || |   |  || |||                                               
CCAACAAGTGAGATGCTACCAAGGAATGAAGTGCTCGGTGGATATATCTTTGTTTGCAACAATGACACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgtgatccaacttaccttatcttctgaatcatcacttggcatattgttccgagaataaattcatgctgctatttacgatgatcaatatcaaataaccttctgatatataatcatatattgctgttctgcag

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 2
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgta-atttcccaatacccttt-----tctagtgttttactgatattcaaactgcaagtaaataactttttgactttcat--cattgttcag---------------------------------------
||  |    ||||  || |||||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||| | ||  | || || |||||||  ||  ||  | || |||     || | || |  |||| | |  |   |      ||| || | | |   ||| ||  || |||  |                                        
CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgttatcccgtcccttttagaaatcaaatgata-actgttctggattttttttaaaaaaaaatatatagttttgatgccagtgtgtaattcgataatggtatctcaagatctattgctcttctgcag

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 2
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgta-----atttcccaatacccttttctagtgttttactgat---attcaaactg--caagtaaataactttt-----tgactttcatcattgttcag----------------------------------
||  |    ||||  || |||| ||| ||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||  | ||  | || || |||||||      |||      | | |    ||    || |   ||   ||   |||||  |  | |||| | ||||     |  | |  ||  |  ||  |                                  
CCGACGAGCGAGATGCTGCCGAAGAACGAAGTCCTTGGTGGGTACATCTTTGTCTGCAACAACGATACCATGCAGGAGGACCTCAAGAGGCAGCTTTTTGgtatgtctttttttttggatcttgccatatcccttgaggaatcaaatggtaactgttctggaaaatcagttttgatcctagcgtatatactaatttggtaatggtgccttaagatctgttgctcttctgcag

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G06100.1 (Glycine max), 5'ss of exon 2
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaatacccttttctag-----tgttttactgatattcaaactgcaagtaaataactttttga---------ctttcatcattgttcag---
|||||| ||||||| || ||| | ||||| || ||||| || ||||||||||| || |||||||| || |||||||| ||  |||||||||| || ||||||   | |  | ||    ||    |     | |||| ||    |  |   |   | | ||  ||||  |||         ||||||   || ||      
CCTGCTGCGGAGACACTCCCGCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgtgtgcttattagttattaaatgacatctatttttctatcttgaatgttattaatcaaatacttcatgatgactgactctttcaatgttttttgatag

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA19G25870.1 (Glycine max), 5'ss of exon 2
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaatacccttttctag-----tgttttactgatattcaaactgcaagtaaataactttttgact-ttcatcattgttcag-----------
|||||| ||||||| || ||  | ||||| || ||||| || ||||||||||| || |||||||| || |||||||| ||  |||||||||| || |||||| | | |  | ||    ||    |     | |||| ||    |  | | |   | | ||  ||||  |||    | ||  ||  |  |           
CCTGCTGCGGAGACACTCCCCCGCAATGAGGTGCTTGGAGGATACATCTTTGTCTGTAACAATGACACAATGCAGGAAGACTTGAAACGTCAGCTATTTGgtgagtacttattagttattaaatgacatctatttttctatcttgaagattattaatcaaatacttcatgatgactgattctttctatgttttttgatag

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv14s0068g02040.t01 (Vitis vinifera), 5'ss of exon 2
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaat-------ttcccaatacccttttctagtgttttactgatattcaa-actgcaagtaaat-aactttttgactttcatca--ttgttcag------
|||||||| ||||| || ||  | ||||| |||||||| || ||||||||||| || ||||||||||| |||||||| ||| |||| || || || |||||||||       |||    |     ||       ||| ||| || | |    |||  |  |  | |    ||| ||  |||| |  |  |  |       
CCTGCTTCAGAGACACTCCCTCGAAATGAGGTTCTTGGAGGGTACATCTTTGTGTGTAACAATGATACCATGCAGGAAGATTTGAAGCGACAACTATTTGgtaatagtgattttcttgctttatattctcctcatttaacttatgtactttgctgggaacagttcaggcattttacactcattaactcatataatatgtg

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaatacccttttctagtgttttactgatattca-aactgcaagtaaataactttttgactttcatcattgttcag
||  | |||||||  || ||  ||||||||   |||||||| || ||||||||||||||||||||||| ||||| |||||  | || || || ||||||||||| | | |  |     |||||     |||  |  ||   |  |||| |||    |   |||||   || |       |||||
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgct----ttcag

upper sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ18285 (Selaginella moellendorffii), 5'ss of exon 1
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaat-acccttttctagtgttttactgatattcaaactgcaagtaaataactttttgactttcatcattgttcag
||  | |||||||  || ||  ||||||||   |||||||| || ||||||||||||||||||||||| ||||| |||||  | || || || ||||||||||| | | |  |     ||||   || |||    |    |   |||| |||    |   |||||   | |  |     |||||
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttttttttctgtctttcttcgtagctatgactgaaagc---ttgttttttttttcttttgcgctttcag

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|124811864|gb|EH896730.1|EH896730
EST:     TGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTG                         GTTTACCTCCAAGATAC
genomic: TGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttccc ... cattgttcagGTTTACCTCCAAGATAC
EST: gi|164192414|gb|ES028420.1|ES028420
EST:     CAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTG                         GTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAACACCTGGATTGC
genomic: CAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttccc ... cattgttcagGTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAACACCTGGATTGC
EST: gi|125188215|gb|EL203169.1|EL203169
EST:     ACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTG                         GTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAA
genomic: ACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttccc ... cattgttcagGTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAA
EST: gi|125113458|gb|EL164268.1|EL164268
EST:     TGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTG                         GTTTACCTCCAAGATACAGAGACT
genomic: TGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttccc ... cattgttcagGTTTACCTCCAAGATACAGAGACT
EST: gi|125230184|gb|EL244269.1|EL244269
EST:     TGTTTGCAACAATGATACTATGCAGGAGGATATG-AACGTCACCTCTTTG                         GTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAACA
genomic: TGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttccc ... cattgttcagGTTTACCTCCAAGATACAGAGACTCTGTTCGAGCTATAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaatacccttttctagtgttttactgatattcaaactgcaagtaaataactttttgactttcatcattgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT