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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacaatttgattatgaattaatgataaacagaaaatcattgtttcacattaaactccatggtgacctttttttggatttgattctttttttatctttagTTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAGAAAATTGCAAGCAGATTGAATTAGAAAAAAAGAGAGCAGATAAGGAAGC

Basic information

species Glycine max
transcript GLYMA17G33930.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G33930.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 19
aaacaatttgattatgaattaatgataaacagaaa-atcattgtttcacattaaact-ccatggtgacctttttttggatttgattctttttttatctttagTTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAGAAAATTGCAAGCAGATTGAATTAGAAAAAAAGAGAGCAGATAAGGAAGC
   |||   ||   | |  | ||| |    |  |     | || || |   ||  ||    || | |   | |||    ||   | |  ||  | | |  |||||| |||||||| |||||||||||||||||||| | |   || ||||| ||||| ||||||||| ||||||| || |  |||| |||| | || |||||
--ccaaacagagcttcagatgatgctgtttaccattgggactgcttgattatacgctgttttgtttaaagtgtttcattttctctccacttgatttttgcagTTGTTTCTACTCTTCTCAACTTTGTGAGAATGTTTACACGGGCACATGAGGAAAACTGCAAGCAGCTTGAATTTGAGAGGAAGAAAGCACAGAAAGAAGC
















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|42723146|gb|CK769045.1|CK769045
EST:     GTGAAGATCCAGCACGTGTCCCATTTGAACAAG                         TTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAG
genomic: GTGAAGATCCAGCACGTGTCCCATTTGAACAAGgtaactagct ... ttatctttagTTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAG
EST: gi|18039236|gb|BM307530.1|BM307530
EST:     ATTGGCTTTGTACTTTGGTGAAGATCCAGCACGTGTCCCATTTGAACAAG                         TTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAG
genomic: ATTGGCTTTGTACTTTGGTGAAGATCCAGCACGTGTCCCATTTGAACAAGgtaactagct ... ttatctttagTTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAG
EST: gi|23734926|gb|BU765717.1|BU765717
EST:     ATTGGCTTTGTACTTTGGTGAAGATCCAGCACGTGTCCCATTTGAACAAG                         TTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAG
genomic: ATTGGCTTTGTACTTTGGTGAAGATCCAGCACGTGTCCCATTTGAACAAGgtaactagct ... ttatctttagTTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacattaaactccatggtgacctttttttggatttgattctttttttatctttagTTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAGAAAATTGCAAGCAGATTGAATTAGAAAAAAAGAGAGCAGATAAGGAAGC
                               atttgat  putative branch site (score: 5)
                                tttgattcttttttta  CT-rich tract
                      tttttttggatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacaatttgattatgaattaatgataaacagaaaatcattgtttcacattaaactccatggtgacctttttttggatttgattctttttttatctttagTTGTATCTACTCTCCTCAACTTTGTGAGAATGTTCATAAAAGCGCATGAAGAAAATTGCAAGCAGATTGAATTAGAAAAAAAGAGAGCAGATAAGGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - -gataaac
- - - - - - - - - - - - - - - -gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatttg