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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatctatgttttcatcccaagtcctatactcctatcgttagtccatgttacaaacttgataataaattccttagatttatggatttgcaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA

Basic information

species Glycine max
transcript GLYMA19G38450.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G38450.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 3
aaatctatgttttcatcccaagtcctatactcct--atcgtta---gtccatgttacaaacttgataataaattccttagatttatggatttgcaattgaaac-agGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA
|||||| |||  |  |||  | | | | | |  |  ||| |||   |  |    ||| |  |   |   |||        | | ||||| |  | |||||  | |||||||| ||||||| |||||  | || ||||||||||| | |  ||| || |||||||| ||| |||| ||||||||||| |||||||| ||  | || |
aaatctttgtcatattcctgaattccaaatttatggatcattaaaaggtctcagtacgagttgccttgcaaagct-----aatgatggagtc-cgattgatgccagGTTGAAGCAAAGAAGTTTGGGATGCTGGCAAATTGGCAGCGGGAGTTCACAATGGAAGACATATTGACGCAGCTGAAGAAAGAAATGGCAGCCCCCCACA
















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|10232200|gb|BE801079.1|BE801079
EST:     AGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAGAGAAATTGGGTCT
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCT
EST: gi|120532072|gb|EH260205.1|EH260205
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|298194351|gb|HO040999.1|HO040999
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|298191697|gb|HO035779.1|HO035779
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|7684987|gb|AW755635.1|AW755635
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|23726374|gb|BU761179.1|BU761179
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGNCAACAGAAGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|7042450|gb|AW472344.1|AW472344
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTGACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|9819465|gb|BE554978.1|BE554978
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|298175656|gb|HO015175.1|HO015175
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|298179361|gb|HO027832.1|HO027832
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAGTTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|6071041|gb|AW100428.1|AW100428
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|8826260|gb|BE209990.1|BE209990
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTT
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTT
EST: gi|13478519|gb|BG507961.1|BG507961
EST:     TTTCATTCACGGATCAATATGNACTTGTGTTAATCATGAANACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTAC
genomic: TTTCATTCACGGATCAATATG-ACTTGTGTTAATCATGAA-ACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTAC
EST: gi|23063958|gb|BU578731.1|BU578731
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|10231884|gb|BE800772.1|BE800772
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|13481901|gb|BG511244.1|BG511244
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|298170303|gb|HO018927.1|HO018927
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|9900251|gb|BE609219.1|BE609219
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|27427102|gb|CA938622.1|CA938622
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|298172821|gb|HO019805.1|HO019805
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|6725867|gb|AW310266.1|AW310266
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|16348942|gb|BI974537.1|BI974537
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|8826180|gb|BE209840.1|BE209840
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCANATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
EST: gi|13311453|gb|BG405104.1|BG405104
EST:     GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTG                         GTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC
genomic: GGTTTCATTCACGGATCAATATGACTTGTGTTAATCATGAAACTGGAGTGgtacagttca ... attgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttacaaacttgataataaattccttagatttatggatttgcaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA
         acttgat  putative branch site (score: 5)
              ataataaattccttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatctatgttttcatcccaagtcctatactcctatcgttagtccatgttacaaacttgataataaattccttagatttatggatttgcaattgaaacagGTTGAATCAAAGAAATTTGGTCTTCTTGCAAATTGGCAACAGAGGTTTACCATGGAAGATATACTGACCCAGCTGAAGAAGGAAATGGCGGCTTCACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - -catccca
- - - - - - - - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggatttg