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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCCAGAAGTTGGTGCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgattgagttggtcggaaaagcctgtattgtttatcttaaaagtttatcaaaagcatttttgtttgctgcataggtaattctcatgttgc...

Basic information

species Glycine max
transcript GLYMA08G35510.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G35510.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os02g07070.1 (Oryza sativa), 5'ss of exon 14
-GGTCCAGAAGTTGGTGCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgat---------------tgagttggtcggaaaagc---ctgtattgtttatctt--aaaagtttatcaaaagcatttttgtttgctgcatag-gtaattctcatgttgc------------------------------------------
  |  |||  | |  ||||||||| || || |||||||||||||||   || || |||||||||||| | || || || || || |||||||||||||| ||||||||| |||                 |||     || ||||  |   |  | |   || | ||  ||| ||||  |||      |||| |||     | |  ||      |||||                                             
CAGAGCAGTGGCTC-TGCTCCACAGTCTGGATTTGTTTGGGATGAAAAGTCTGGTTATTACTATGATTCAGCCTCAGGATTCTATTATGATGGAAATACCGgtatgtatattgccacaattttcttactatgatcaattcagaaatactttccatgtgacttgtttttgaaatgttttccaattttccttttttttaaaaaaaaatgtttgctccatgtcaattgttaaagtattacagtttataaccttgtatttgttttcag

upper sequence: GLYMA08G35510.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G173777_T01 (Zea mays), 5'ss of exon 13
GGTCCAGAAGTTGGTGCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgattgagttggtcggaaaa--gcctgtattgtttatcttaa--aagtttatcaaaagcatttttgtt-tgctgcataggtaattctcatgttgc-------------------------------------
     ||| |   |  |  |||| || || |||||||||||||||  ||| || || ||||||||| |||| ||||| || || |||||||||| |||||||| |  | |   |  | |   ||   |    |  |  | |    | | | |  || |||      | | || | |||  |   |||   | |||    | ||                                       
CAAAAAGATGGCAGCACAGCACAGTCGGGATTTGTTTGGGATGAAAAATCTGGTTACTACTATGATTCTGCATCTGGATTCTATTATGATGGAACTACTGgtaagcctttgagtctactgcatcaatattttgtttaaacttaacaccatgaccaattttgctggtaacgttatggttacggatcatttttcatttatgttttaaattttaatatgtaatcttgtattcttgtttgttgcag

upper sequence: GLYMA08G35510.1 (Glycine max), 5'ss of exon 12
lower sequence: AT3G54230.2 (Arabidopsis thaliana), 5'ss of exon 14
GGTCCAGAAGTTGGTGCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgattgagttggtcggaaaagcctgtattgtttatcttaaaagtttatcaaaagcatttttgtttgctgcataggtaattct----catgttgc
     ||    |  ||||||||| || |||| ||| |||||||||||||| || |||||||||||||| |||||||| |  ||||| ||||||||| | |||  | || ||  ||   ||| |   |      | | |   ||   |  |  |||    |   |||  | |  || |   ||  |  |||      |||||   
CAGAAAGGGACTTCTGCTCCACAGTCTGGCTATGTGTGGGATGAAGCATCTGGTTATTACTATGATGCGGCTTCTGGATACTACTACGATGGAAATTCAGgtcggcat-ttacttatattgtt---atttatttctttgaattgattgtatggttgggtagctgcagctctaattcccatatctggcattgcaaaacatgtaat

upper sequence: GLYMA08G35510.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv02s0012g00870.t01 (Vitis vinifera), 5'ss of exon 12
GGTCCAGAAGTTGGT---GCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgattgagttggtcggaaaagcctgtattgtttatcttaaaagtttatcaaaagcatttttgtttgctgcataggtaattctcat--gttgc-
   | | | | ||||   |||||||| || || ||||| ||||||||| |||| |||||||| |||||||||||||||||||| |||||||||||||| || |||  ||||||||  ||  ||| |           ||  |||  | ||  | | |||  ||  |  |||   |     |  ||| | ||||||  |  |||   
---CAAAAGGATGGTTCAGCTCCACAGTCTGGTTTTGTGTGGGATGAAACATCTGGCTATTATTATGATGCTGCTTCTGGGTTCTACTATGATGGAAACACAGgttggtatcttgtgtgc-ttgcttatttggaagcgtcctgtgaaactgcagaattttgcatga--attgcagacctattaataagcaattctactcagttctg

upper sequence: GLYMA08G35510.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S40_67V6.1 (Physcomitrella patens), 5'ss of exon 12
GGTCCAGAAGTTGGTGCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgattgagttggtcggaaaagcctgtattgtttatcttaaaagtttatcaaaagcatttttgtttgctgcataggt---aattctcatgttgc---
||       | ||||||||| || ||| | ||||||||||||||||| || || || || ||||||||| | || || |||||||||||||| |||   ||||   |  | | |||     |||  |||||||| | ||| ||    ||||  |   |  |    |   || | |  || | || |   |  | |||  | |    
GGAGGTAGTGGTGGTGCTCCTCAGTCAAGTTTTGTTTGGGATGAAGCCTCTGGATACTATTATGATGCTTCCTCGGGTTTTTACTATGATGGGAATCGAGgtagcaacttcggttgt-ccagtc--aaaagcctct-ttgattgc--taaatttgccttgagttaagccttatgttgtgtacagatctgagatttcaattagaatg

upper sequence: GLYMA08G35510.1 (Glycine max), 5'ss of exon 12
lower sequence: PP1S32_317V6.1 (Physcomitrella patens), 5'ss of exon 12
GGTCCAGAAGTTGGTGCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgattgagttggtcggaaaagcctgt-attgtttatcttaaaagtttatcaaaagcatttttgtttgctgcataggtaattctcatgttgc
|    ||| | ||| ||||| || ||||| ||||||||||||||||| || || ||||| |||||| || | || || |||||||||||||| |||   |||| | |   ||||  | |  |||  ||    || | || | |   |||       | | || |  |   | || |  | | |  || ||  | || | | 
GAGGGAGATGGTGGCGCTCCTCAGTCAGGTTTTGTTTGGGATGAAGCTTCTGGTTATTATTATGATTCTTCCTCGGGATTTTACTATGATGGGAATCAAGgtaagaactgtgatc-attaagtcaaaaccctctttgatcgctacacttctgctgatttgaatatgaaagtggtgtaatccttctgtcatgtttatttcgt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCCAGAAGTTGGTGCTCCACAATCAGGCTTTGTTTGGGATGAAGCATCGGGCTATTACTATGATGCTGCTTCTGGGTTTTACTATGATGGAAATACTGgtatgtatcttgattgagttggtcggaaaagcctgtattgtttatcttaaaagtttatcaaaagcatttttgtttgctgcataggtaattctcatgttgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA