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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caccacttgccctagcgttctagtcttttttatagataaagtccacagctttcgctgtttatttttaggagcttttgactttttgtttattgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCATGTG

Basic information

species Glycine max
transcript GLYMA16G27020.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27020.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 5
caccacttgccctagcgttctagtcttttttatagataaagtccacagctttcgctgtttatttttaggagctttt---gactttttgtttattg-----taaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCATGTG
      |||    |   ||  ||  || ||  | ||  |  || | |  ||| || |  |||| |     | | ||   |  |||  | ||| ||     |  ||||||||| |||||||||||||| || ||||||||||||||||  ||||| | |||||
------ttgtaggaaaattgaagcattgttctttga--acttctatacattttgcagactattgtataatgttcttttcgggtttaagcttagtgactgatgtaacagGTGGACATGAACTCAGCAAAACAACTGGGAATGCTGGTGGCAGAGTTGGATGTG
















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|31470014|gb|CD412042.1|CD412042
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGCTCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|31470725|gb|CD412753.1|CD412753
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|7146773|gb|AW508695.1|AW508695
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|209702151|gb|BW677951.1|BW677951
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|6747004|gb|AW317460.1|AW317460
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|31472202|gb|CD414230.1|CD414230
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|209702150|gb|BW677950.1|BW677950
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|298171130|gb|HO016162.1|HO016162
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTA
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTA
EST: gi|10255867|gb|BE823633.1|BE823633
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|298197096|gb|HO041839.1|HO041839
EST:     AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCAT
EST: gi|15200962|gb|BI424621.1|BI424621
EST:     AATCGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGG                         GTGGGCATGAACTCAGCAAGAC
genomic: AATTGGAAGGGCCGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGGGgtaagatttt ... tgtaaaacagGTGGGCATGAACTCAGCAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagctttcgctgtttatttttaggagcttttgactttttgtttattgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCATGTG
                           ttttgac  putative branch site (score: 3)
                                  tttttgtttattgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caccacttgccctagcgttctagtcttttttatagataaagtccacagctttcgctgtttatttttaggagcttttgactttttgtttattgtaaaacagGTGGGCATGAACTCAGCAAGACTACTGGGAATGCTGGTGCAAGAGTAGCATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - -cttgccc
- - - - - - - - - - - - - - - - - - - - - ccacagc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttttg