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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccaggtgttctgtttcatcactgttgatgtctgtatcactgtgcag

Basic information

species Arabidopsis thaliana
transcript AT4G26510.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 5'ss of exon 12
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccaggtgttctgtttcatca--ctgttgatgtctgtatcactgtgcag
||||||||| ||||||||||| || || ||||| ||||||||||| || || |||||||| || |||||||| ||||| ||||||||  |||||||    |  | |      |||      |  ||||    ||  |||   |  | |  |||  ||  || |||||
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAGgtttg-gtttaatctacttttggcattatttgttggagttagtcaaattactaagctcttgattcct-tgcag

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 5'ss of exon 12
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaa---cgagtcactcctatttcattc-caggtgttctgtttcatcactgttgatgtctgtatcactgtgcag
||||||||| ||||||||||| || || ||||| || |||||||| || || |||||||| || |||||||||||||| ||||||||  |||||||        |   |||  | | |  ||    || |||  ||  ||| ||||   |  |||  ||  || |||||
TGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAGgtttggtttaatctacttttgtattgtttgttggagttaagtcacattactg---agctcttgattcct-tgcag

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G034143_T01 (Zea mays), 5'ss of exon 12
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccaggtgttctgtttcatca--ctgttgatgtctgtatcactgt-gcag
||| || |||||||||||||||||||||||||| || |||||||| ||||| |||||||| || |||||  | ||||| |||||||| ||||||||    || | |     |  |  | ||| |||||  | |   |||   |  | |  ||| | |   | | ||||
TGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAGgtc--tgatttatc---aacttttgccatgtgttagggtgagtcaaattactaagatctattttttttttgcag

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GRMZM2G169462_T01 (Zea mays), 5'ss of exon 11
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccaggtgttctgtttcatca--ctgttgatgtctgtatcactgtgcag
||| || || |||||||||||  |||| ||||| || |||||||| ||||| |||||||| || |||||  | |||||||||||||| ||||||||    |  | |     |  |  | ||| |||||  | |   |||   |  | |  |||  ||  || |||||
TGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAGgtc--tggcttatc---aacttttgccatgtgttagggtgagtcaaattactaagatctaaatttctttgcag

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA14G01480.1 (Glycine max), 5'ss of exon 9
------TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccagg----tgttctgtttcatcactgttgatgt---ctgtatcactgtgcag-------------------------------
      ||| ||||| ||||| ||||| ||||||||||| ||||||||||||||||| ||||| || || ||||| ||||||||||||||||||||||||||     | |  |   |  ||   |  |      || |   |||||| |    | |  |   |||| |   |  |                                  
TTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatttgcgtgtgcttgggtatactgttttgattcatttcatgatcactaacttgtcctgttttttttggtgattcactaacttgtcctttgattattgagcag

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA02G47270.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctat--ttcattccaggtgt------tctgtttcatcactgttgatgtctgtatcactgtgcag-------------------------------
||| ||||| ||||| |||||  |||||||||| ||||||||||||||||| ||||| || || ||||| ||||||||||||||||||||||||||     |        | |  ||   |  |  |||      |   |||||| |    |  ||||| | |   |  |                                  
TGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAGgtttgtcatctgtgtgtgtgcttgggtatacctgtgtcggattcatttcatgatcactagtgtcttttttttttggtgattcactaacttgtcctttgattattgagcag

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA18G08180.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtc-actcctat--ttcattccaggtgttctgtttcatcactgttgatgtctgtatcactgtgcag---------------
||| ||||| ||||||||||| ||  ||||||| || |||||||||||||| ||||| ||  |||||||||||||||||||||||||||| ||||| |     ||  |  ||||  ||   | ||  |  ||||||||||   || ||||      |||  | |||                 
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGGttagttcatctgcatctatggtttggtacaaat-ctctgtttcatt--tggtgatactgacatc-ttatgctttgattaatgatcagc

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: GLYMA08G45270.1 (Glycine max), 5'ss of exon 12
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtc-actcctat--ttcattccaggtgttctgtttcatc----actgttgatgtctgtatcactgtgcag-------
||| ||||| ||||||||||| ||  ||||||| || |||||||| ||||| ||||| ||  |||||||||||||||||||||||||||| ||||| |     ||  |  ||||  ||   | ||  |  |||||||||        |  |||| |||    |  ||  ||        
TGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGgttagttcatctgcatctatggtttggtacaaat-ctctgtttcacttggtgatactgatatcttatgctttgatcaatgatcag

upper sequence: AT4G26510.2 (Arabidopsis thaliana), 5'ss of exon 12
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 5'ss of exon 12
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgt-aaacgagtcactcctatttcat-tccaggtgttc--tgtttcatcactgttgatgtctgtatcactgtgcag-------------------------------------------------
||||||||| ||||||||||| || ||||||||||||||||||||||| || |||||||| || || || || ||||| || || ||||| |||||   ||   || |||    |   | |||  || | |  ||      |||  |  |    || ||        |                                                  
TGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGgttggacagatctctctctctctgtatccttgtctcccatgcacagacacactacacacatgcatgcacagatatctatctactaacattttgactgtttttttatgtttcaatgactggacag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAGgtaaacgagtcactcctatttcattccaggtgttctgtttcatcactgttgatgtctgtatcactgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA