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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatggtttcagtcgcagatatcgaattgtttatatctatttttgggccttaacattatcctgatattagaatgttgccatgtgcgacttcacttgtccagAATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAATGGGCAGACAATAATATGGATGCTTACACAGCTGCTGCTATTAAAGTTG

Basic information

species Glycine max
transcript GLYMA07G01950.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01950.1 (Glycine max), 3'ss of exon 11
lower sequence: AT1G52150.1 (Arabidopsis thaliana), 3'ss of exon 11
aatggtttcagtcgcagatatcgaattgtttatatctatttttgggccttaacattatcctgatattagaatgttgccatgtgcgacttcacttgtccagAATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAATGGGCAGACAATAATATGGATGCTTACACAGCTGCTGCTATTAAAGTTG
             |    |     ||| ||| |||  ||     |   | |   ||       | ||  |   |     | || || ||  |   | |||||||| || || || || || ||| |||||||| |||||||||| ||||||||||| ||||| || || ||||| ||   ||| || ||  ||||||| |
-------------gtcagtgcaccattttttttatagatcaactga--tgattgtttcaacactttttcaccttctttttatgggattttgcacctacagAATGTTCCTCCGGCGATCCTGCTTCGGTTTCTGAGGGAGCATAGGTCAGAATGGGCTGACAACAACATTGATGCGTATCTAGCAGCAGCAGTTAAAGTAG

upper sequence: GLYMA07G01950.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv09s0002g03740.t01 (Vitis vinifera), 3'ss of exon 11
aatggtttcagtcgcagatatcgaattgttt-atatctatttttgggccttaacattatcc-tgatattagaatgttgccatgtgcgacttcacttgtccagAATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAATGGGCAGACAATAATATGGATGCTTACACAGCTGCTGCTATTAAAGTTG
  ||||    || |  |   || | ||  || ||||  || |||  |  | ||   | |   |  | ||   ||||| |  |   | | ||  | | | ||||||||||| || || || || |||||||||||||||||||| |||||||||||||||||||| ||||| ||||||||| ||||||| ||| | |||||||
-ttggtcatggttgggggcctccattttcttgatattaatctttttgtttaaaggctttatatcttgttctgatgtt-ctgttcactatttatcattttcagAATGTGCCTCCAGCAATACTTCTTAGGTTTCTGCGGGAGCACAGATCAGAATGGGCAGACAACAATATTGATGCTTACTCAGCTGCAGCTGTAAAAGTTG

upper sequence: GLYMA07G01950.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S15_11V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------------------------------------------aatggtttcagtcgcagatatcgaattgtttatatctatttttgggccttaacattatcctgatattagaatgttgccatgtgcgacttcacttgtccagAATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAATGGGCAGACAATAATATGGATGCTTACACAGCTGCTGCTATTAAAGTTG
                                                                                     | |   |||        || | ||   |  |  || | | ||      ||  || |  |   || |    |||      ||   |  |    || |||||||||| || || ||  | ||| |  | ||  ||||||||||||||||||||||||||||  || | || || ||  |  ||||  | ||  ||  || ||
gttctccttcaggcattcgcttctgtttttaagcccttggtactggcacgtggcatgagtgttcggtatcttttaatgtggatttactaaattcttcgaagtatgtagaggcgggtgaatgtttgttcaaaatttttcact--cgaaatttggagatgaaatggtgcctgtgtcttgttttccagAATGTACCGCCGGCATTACTCATACGATTCTTGCGGGAGCATAGATCAGAATGGGCAGATCATGAAATCGACGCAAATGCAGCCACAGCATTTCGAGGTG

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|151398017|gb|EV267895.1|EV267895
EST:     CGTCTGTCAGTAATGCAGTGCTATGTGCCAAAGCATCGATGCTATTACAG                         AATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAA
genomic: CGTCTGTCAGTAATGCAGTGCTATGTGCCAAAGCATCGATGCTATTACAGgttaggatgc ... acttgtccagAATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAA
EST: gi|37997336|gb|CF808925.1|CF808925
EST:     CGTCTGTCAGTAATGCAGTGCTATGTGCCAAAGCATCGATGCTATTACAG                         AATGTGCCCCCTGCCATTCTCCTT
genomic: CGTCTGTCAGTAATGCAGTGCTATGTGCCAAAGCATCGATGCTATTACAGgttaggatgc ... acttgtccagAATGTGCCCCCTGCCATTCTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttaacattatcctgatattagaatgttgccatgtgcgacttcacttgtccagAATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAATGGGCAGACAATAATATGGATGCTTACACAGCTGCTGCTATTAAAGTTG
            tcctgat  putative branch site (score: 3)
                                         cttcactt  putative PPT
                 atattagaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatggtttcagtcgcagatatcgaattgtttatatctatttttgggccttaacattatcctgatattagaatgttgccatgtgcgacttcacttgtccagAATGTGCCCCCTGCCATTCTCCTTAGGTTTCTGCGGGAGCATAGATCAGAATGGGCAGACAATAATATGGATGCTTACACAGCTGCTGCTATTAAAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - ccttaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgcc