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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtttggtgaataattttgaagtgtttaattttgaattagatgtttcattggttcacatttgtattgtaatggtgaataattcatttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT

Basic information

species Glycine max
transcript GLYMA13G37050.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G37050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G825437_T04 (Zea mays), 3'ss of exon 1
---tctgtttggtgaata--attttgaagtgtttaattttgaattagatgtttcatt--ggttcacatttgtattgtaatggtgaataattcatttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT
   | |   ||||   ||  || || || |  ||  || ||| |  ||| |||  ||  || | || ||      ||  || ||    || |        | |||||| ||     ||||  | |  || || || ||  |||| ||||| || || ||||||||||| ||||| |||||||||||||| || ||||||||||| ||
ttgttttcatggttgctatcatgttcaactaattg-ttctgactgtgattttttcttttggataactttcagtccgtg-tgatgtgctatcc-----tcctttgcagTTGATTTGCTGAAGCCCGATGCCACGGTGATCTTGCGCAATGCCAAAATCGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAATGGGGGCGGAT

upper sequence: GLYMA13G37050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067522_T01 (Zea mays), 3'ss of exon 1
tctgtttggtgaataattttgaag---tgtttaattttgaattagatgtttcattggtt-cacatttgtattgtaatggtgaataattcatttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT
  ||  |  |   ||  ||||| |   |||  |  |     ||     ||   |||  |   |||||||  ||   |  |||     || | | |||||  |||| |||    ||||  |    || || || ||  |||| ||||| || || ||||||||||| ||||| |||||||||||||| || || |||||||| ||
--tggcttctttttatctttgatgtcatgtggacgtcatggttgatgattgttttgactgtgcatttgtcctgggcttatgatgtgctcttctcctttg--cagTTGACTTGCTGAAGCCCAATGCGACAGTGATCTTGCGCAATGCCAAAATAGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAGTGGGGGCGGAT

upper sequence: GLYMA13G37050.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G28440.1 (Arabidopsis thaliana), 3'ss of exon 1
tctgtttggtgaataattttgaagtgtttaattt--tgaattagatgtttc-attggttcacatttgtattgtaat-ggtgaataattcatttactt-----tgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT
         ||   | |||||   |      |||  || | | |||||  | | || ||  |  |  |  ||| || |||   |  |   | |   |     |||  ||| || | ||||||  | || || || || || ||||| ||| ||| ||| ||||||||||||||  | |||||||| | ||||||||||||||| || ||
---------tgtgaagttttgttataccagttttcgtgcaattgatgtggctactgattagctctaatgatgttattggttttttttgtgtgtgtgtgtgtgtgtatagTTGATCTTATGAAGCCGGGTGCTACGGTGATACTGCGCAATTCAAGGATAGACATGTTCAAGGGTACAATGAGGCTAGGAGTTGATAAATGGGGACGCAT

upper sequence: GLYMA13G37050.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
------tctgtttggtgaataattttgaagtgtttaattttgaattagatgtttcattggttcacatttgtattgtaatggtgaataattcatttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT
      |||| |  |  | | | || |   |   || |     | |     |||    || | | |   || || |  ||||      || |||   |  ||||||||||    |||||  | || || ||||| | ||| || ||||||||||| || |||||||||||||| ||||||||||| |||||||||||||| || ||
atttgttctgctctggtactcaattggtgattcatagtgggtcacttagctttttgggggctaatacaagtctt-tcttggt-----ttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT

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|19935548|gb|BQ080484.1|BQ080484
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|58022150|gb|CX708891.1|CX708891
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|26047748|gb|CA784442.1|CA784442
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|298163086|gb|HO011819.1|HO011819
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|7146979|gb|AW508901.1|AW508901
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|58022462|gb|CX709203.1|CX709203
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|9258840|gb|BE346987.1|BE346987
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TG-ACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|19935546|gb|BQ080483.1|BQ080483
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|15000476|gb|BI321290.1|BI321290
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|193633342|gb|FK582914.1|FK582914
EST:     CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGAGACGAAACCGGAACCATAATCTTCACAGCACGCAACGAACAGGgtaagatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcattggttcacatttgtattgtaatggtgaataattcatttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT
                                         tttacttt  CT-rich tract
                                aataattcatttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtttggtgaataattttgaagtgtttaattttgaattagatgtttcattggttcacatttgtattgtaatggtgaataattcatttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGGCTTGCAGTTGATAAATGGGGGCGTAT

- - tttggtg
- - - - - - - - - -tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatggtg