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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgtttttgttgtttcatacttctttctgagatgctatcagtgatatgatagcgtagctagcctgatctcaaacagcttatttttacaatttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG

Basic information

species Glycine max
transcript GLYMA09G24440.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G24440.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G011893_T01 (Zea mays), 3'ss of exon 5
ttttgtttttgttgtttcatacttctttctgagatgctatcagtgatatgatagcgtagctagcctgatctcaaacagcttatttttacaatttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG
|    ||   | | | || |     ||| |  | |        |  | |    || |   ||   || | |     |  |  | | |||    | || ||     ||  ||||   || | |||  ||| |||||||||||||| ||||||||||||||  | ||||| ||||||||||  ||||   ||||| |  | |
tggcattaccgatatctcttgaacttttatttgctcaccagtttacttttggtgcatgattatgttgttgttgttaatttcctatatactgaatatgcagTGCACGAGTTTTACCCATAAAATGCGAGATGGTTGGGGTCTGGCGACTGATGGAAAAGTTCTTTTTGGCAGTGATGGCACCTCAATGCTGTATAAGCTGG

upper sequence: GLYMA09G24440.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G25720.1 (Arabidopsis thaliana), 3'ss of exon 5
ttttgtttttgttgtttcatact-tctttctgagatgctatcagtgatatgatagcgtagctagcctgatctcaaacagcttatttttacaatttc--tgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG
  ||||  | | | |    |||  | ||||         | || |  ||| || |  |||      |  | ||    |  |||    |   |||||  ||||| ||    |||||||| || |||||||||| || ||||| ||||| || ||||||||||  || |||||||||||||||| ||| ||||| ||||   | |
--ttgtcataggtttaagctaccatgtttccattgcttcaccactt-tattatggactagtattgttattttcttttatattaagcatttgatttcactgtagGTAAAACCATTTAAACATCATATGAAAGATGGATGGGGACTGGCTACCGATGGAAAAGCGTTATTTGGAAGTGATGGCACTTCTACATTATATCGGATGG

upper sequence: GLYMA09G24440.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g01140.t01 (Vitis vinifera), 3'ss of exon 5
---ttttgtttttgttgtttcatacttctt-tctgagatgctatcagtgatatgatagcgtagctagcctgatctcaaacagcttatttttacaatttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG
    | || | || | |  | | |    || | || || |    || | |  || | ||  ||     ||| | | | |   | |  |||||   |   || || | | ||||||||   || |||||   || |||||||| ||||||||| ||||  |||| ||||||||||||||||| | ||| ||| |||||||  |||
ttggtgtgctcttttggaataagatgcattctttgtgaagagtccaattagttgcttgccaag---atctgttatgacatt-catgcttttattctcagtgcagTTTGAGACATTTACTAATCATATGCGGGATGGTTGGGGACTGGCAACTAATGGGGAAGTTTTGTTTGGAAGTGATGGAACTTCGACACTGTATCAGATTG

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|151397440|gb|EV267313.1|EV267313
EST:     ATATGAGCCAAAAAATTTAAGCCAA                         ATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT
genomic: ATATGAGCCAAAAAATTTAAGCCAAgtttgttgct ... atttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT
EST: gi|298173165|gb|HO020149.1|HO020149
EST:     ATTGGTTGCAGAAAGATGGTTTCATATATGAGCCAAAAAATTTAAGCCAA                         ATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT
genomic: ATTGGTTGCAGAAAGATGGTTTCATATATGAGCCAAAAAATTTAAGCCAAgtttgttgct ... atttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT
EST: gi|298199415|gb|HO042778.1|HO042778
EST:     ATTGGTTGCAGAAAGATGGTTTCATATATGAGCCAAAAAATTTAAGCCAA                         ATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT
genomic: ATTGGTTGCAGAAAGATGGTTTCATATATGAGCCAAAAAATTTAAGCCAAgtttgttgct ... atttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT
EST: gi|8826769|gb|BE210499.1|BE210499
EST:     ATTGGTTGCAGAAAGATGGTTTCATATATGAGCCANAAAATTTAAGCCAA                         ATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT
genomic: ATTGGTTGCAGAAAGATGGTTTCATATATGAGCCAAAAAATTTAAGCCAAgtttgttgct ... atttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgatagcgtagctagcctgatctcaaacagcttatttttacaatttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG
                 gcctgat  putative branch site (score: 4)
                                              tttctgt  putative PPT
                                  ttatttttacaatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgtttttgttgtttcatacttctttctgagatgctatcagtgatatgatagcgtagctagcctgatctcaaacagcttatttttacaatttctgtagATAGGGACATTTAAATATGATATGAAAGAGGGTTGGGGTCTGGCAACTGATGGAAAAGTCTTGTTTGGAAGTGATGGCAGTTCAACATTGTATCAATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - -tgttgtt
- - - - - - - - - - - - ctttctg
- - - - - - - - - - - - - - - - - tgctatc
- - - - - - - - - - - - - - - - - - - - - -tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaaac