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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgttatacctgtccctgattagaaaaagctcttctctttgaatgttactgagattgttaggaaatcacttaatttgatctgtcttgtgttgaatttcag

Basic information

species Arabidopsis thaliana
transcript AT5G63980.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G63980.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G09180.1 (Glycine max), 5'ss of exon 2
AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgttatacctgtccctgattagaaaaagctcttctctttgaatgttactgagattgttaggaaatcacttaatttgatctgtcttgtgttga-atttcag---
||||| || |||||| |  ||||||| |||||||| ||||| || || |||||||| || || || ||||||||||||||||||  ||| | | | |||      | |  | |    | | |  ||||   | |  |||      ||| | ||  | ||   |  ||    |||| |    |    
AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttagttt--tat-cttattcctatgcgcatagtgtttgattatatatatgt-gttaatgttg------aataattttttctgcaatagctcacattgacaagctaattg

upper sequence: AT5G63980.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G26250.1 (Glycine max), 5'ss of exon 2
AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgttatacctgtccctgattagaaaaagctcttctctttgaatgttactgagattgttaggaaatcacttaatttgatctgtcttgtgttgaatttcag-
|||||||| |||||| |  ||||||| |||||||| ||||| || || |||||||| || || || |||||||||||||   || |  |  |     ||    |    |   | |  |    ||||  | | | | || | |    |||||   ||||   | | | ||| || | |||    
AAAGTTCAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATGgttgagttatcttttcaaatacttgccatgttatattttgat----gaataatgcagggtttctgatctgatcacaacattt---ccggcatgtttttagtttatta

upper sequence: AT5G63980.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 5'ss of exon 2
AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgttatacctgtccctgattagaaaaagctcttctctttgaatgttactgagattgttag--gaaatcact--taatttgatctgtcttgtgttgaatttcag
||||| ||||||||  |||||||||||||||| ||||| ||||| |||||||| || || || || ||||| ||||||| || | |||| |   | |    |||    ||     | |   |   || ||       | ||||  |   | | |  | ||  |  |  |  ||| |||        
AAAGTGCAAAAGGCGCTGTTGCAATCAGATGTCCAATCTAAATCAGATAAAAGCCCTGTCACAGTGGCTGACTATGgtttgtatcttattcacctgcacatttatttcaa--ctatattgatatctgctatcagctctcttagttgttgttattaatgataggggcaattgtgttttg--------

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|19874586|gb|AU235417.1|AU235417
EST:     AGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG                         GTTCACAAGCAGTTGTTAGTTTAGTCTTAGAAAAAGAGCTCAGTTCTGAAC
genomic: AGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgt ... tgaatttcagGTTCACAAGCAGTTGTTAGTTTAGTCTTAGAAAAAGAGCTCAGTTCTGAAC
EST: gi|116482884|gb|EG525476.1|EG525476
EST:     AGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG                         GTTCACAAGCAGTTGTTAGTTTAGTCTTAGAAAAAGAGCTCAGTTCTGAAC
genomic: AGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgt ... tgaatttcagGTTCACAAGCAGTTGTTAGTTTAGTCTTAGAAAAAGAGCTCAGTTCTGAAC
EST: gi|125267000|gb|EL281085.1|EL281085
EST:     AGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATG                         GTTCACAAGCAGTTGTTAGTTTAGTCTTAGAAAAAGAGCTCAGTT
genomic: AGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgt ... tgaatttcagGTTCACAAGCAGTTGTTAGTTTAGTCTTAGAAAAAGAGCTCAGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTTCAAAAGGCTTTGTTGCAATCAGATGTGCAATCAAAATCTGATAAAAGTCCAGTGACCGTTGCTGATTATGgttagtttgttatacctgtccctgattagaaaaagctcttctctttgaatgttactgagattgttaggaaatcacttaatttgatctgtcttgtgttgaatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT