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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagattggtgaataattttgaagtggttaattttgaattagatgtttcattggttcacttttgtgttatagtggtgaataactcttttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGACTTGCAGTGGATAAATGGGGGCGTAT

Basic information

species Glycine max
transcript GLYMA12G33380.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G33380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G825437_T04 (Zea mays), 3'ss of exon 1
----tcagattggtga-ataattttgaagtggttaattttgaattagatgtttcattggttcacttttgtgttatagtggtgaataactcttttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGACTTGCAGTGGATAAATGGGGGCGTAT
    |   || | ||  || || || || |  ||  | |     |   | |||| || |   |  |||  ||    ||| ||    |  ||  |      |||||| ||     ||||  | |  || || || ||  |||| ||||| || || ||||||||||| ||||| ||||| ||||||||||| ||||||||||| ||
ttgttttcatggttgctatcatgttcaactaattgttctgactgtgattttttcttttggataactttcagtccgtgtgatgtgctatcctcctt-----tgcagTTGATTTGCTGAAGCCCGATGCCACGGTGATCTTGCGCAATGCCAAAATCGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAATGGGGGCGGAT

upper sequence: GLYMA12G33380.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G067522_T01 (Zea mays), 3'ss of exon 1
tcagattggtgaataattttgaagt--ggttaattttgaattagatgtttcattgg--ttcacttttgtgttatagtggtgaataactcttttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGACTTGCAGTGGATAAATGGGGGCGTAT
   |  |  |   ||  ||||| ||   ||  |  |     | |||| ||  || |  |   | |||||  |    |  |||    ||||| | |||||  |||| |||    ||||  |    || || || ||  |||| ||||| || || ||||||||||| ||||| ||||| ||||||||||| || |||||||| ||
--tggcttctttttatctttgatgtcatgtggacgtcatggttgatgattgttttgactgtgcatttgtcctgggcttatgatgtgctcttctcctttg--cagTTGACTTGCTGAAGCCCAATGCGACAGTGATCTTGCGCAATGCCAAAATAGACATGTTCAAAGGATCAATGAGGCTTGCAGTGGACAAGTGGGGGCGGAT

upper sequence: GLYMA12G33380.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G33845.1 (Arabidopsis thaliana), 3'ss of exon 1
-tcagattggtgaataattttgaagtggttaattttgaattagatgtttcattggttcacttttgtgttatagtggtgaataactcttttactttg--tgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGACTTGCAGTGGATAAATGGGGGCGTAT
 |  | |  |    |  |  | || ||||  |||   | |  |    ||   |  ||      |   |   |||  |   |   | || |  | ||  |||||||||    |||||  | || || ||||| | ||| || ||||||||||| || |||||||||||||| ||||| ||||| || ||||||||||| || ||
atttgttctgctc-tggtactcaattggt-gattcatagtgggtcacttagctttttgggggcta-atacaagtctttcttggtttttattgtgtgggtgcagTGGAATTGATGAAACCAGGAGCTACTGTGAATCTTCGGAATGCAAAGATAGATATGTTCAAGGGATCAATGAGGCTTGCTGTTGATAAATGGGGTCGCAT

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|20207619|gb|BQ133708.1|BQ133708
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|8284407|gb|BE021966.1|BE021966
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|23727873|gb|BU761970.1|BU761970
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|254317296|gb|GR826241.1|GR826241
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTC
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTC
EST: gi|254317295|gb|GR826240.1|GR826240
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|7233353|gb|AW568700.1|AW568700
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|14196027|gb|BE657809.2|BE657809
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|24136064|gb|BU926574.1|BU926574
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|8285421|gb|BE022980.1|BE022980
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|298168099|gb|HO013362.1|HO013362
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|7146704|gb|AW508626.1|AW508626
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|10255856|gb|BE823622.1|BE823622
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
EST: gi|298185421|gb|HO030634.1|HO030634
EST:     CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGG                         TGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG
genomic: CGTCGGCGACGAAACCGGAACCATAATCTTCACCGCTCGCAACGAACAGGgtacgatgat ... ctttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcattggttcacttttgtgttatagtggtgaataactcttttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGACTTGCAGTGGATAAATGGGGGCGTAT
                               gaataac  putative branch site (score: 2)
                                     ctcttttactttgt  CT-rich tract
                                        ttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagattggtgaataattttgaagtggttaattttgaattagatgtttcattggttcacttttgtgttatagtggtgaataactcttttactttgtgcagTGGACCATATGAATGCTGGCGCAACTGTAATTCTGCGTAATGCAAAGATTGACATGTTCAAGGGATCTATGAGACTTGCAGTGGATAAATGGGGGCGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - attggtg
- - - - - - - - - -tgaagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtggtg