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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattgagtcagtctaagctgaggagttgcataacaattaaaaataaataaatgttgttattgaccatgtattattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

Basic information

species Glycine max
transcript GLYMA12G37100.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
tgattgagtcagtctaagctgaggagttgcataacaatta--aaaataaataaatg--ttgttattgaccatgta-ttattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
       ||   |  |     |   |||| ||     ||      || | | | |   ||    |||||| |  | ||   || |  |       |   ||  |||| || ||||| || ||||||||||| ||||| ||||||||  |||||||||| || ||||||||||| |||||||| || ||||| |||||| | || |
-----atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 18
tgattgagtcagtctaagctgaggagttgcataacaattaaaaataaataaatgtt---gttattgaccatgtattat-tatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
   |    |||  ||  | |      |  ||   | || |  | |   | |||||       |   |   || |||   | |       |   || |   | |||| || ||||| || |  |||||||| ||||| |||||||| || |||||||| |||||||||||||| ||||| || || ||||| || ||||| || |
--ctcatatcaacct--gttccactttcccacggccatgattattttttgaatgtgtcaaacacaaattttgaattgcctgtgacacaattactctcccttaagGATACGATGGCCCGGAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAG

upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G870253_T01 (Zea mays), 3'ss of exon 2
tgattgagtcagtctaagctgaggagttgcataacaattaaaaataaataaatgtt--gttattgaccatgtattattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
   || |      ||||       ||     |  || |||||  ||   |||       | | | |   |    |    | |     | | | | || | |||| ||||||||||| || |||||||| ||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| ||||
--ttttatcttacctaaaggctaaagcatgttttcatttaaatgtatccaaacacaagatcacttattttactcttcattctacaactcttttctgtttaagGATACAATGGCTCGGAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTG

upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 18
------------------------------------------------------------------------------------------tgattgagtcagtctaagctgaggagt-tgcataacaattaaaaataaataaatgttgttattgac---catgtattattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
                                                                                          | ||   || | |  | |       || |   |   |  |   |||| | | || ||   ||| |    ||   | ||  || |     || ||        |||| || ||||| || ||||||||||| ||||| ||||||||  |||||||||| |||||||||||||| ||||| || || ||||| |||||| | || |
gtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------------------tgattgagtcagtctaagctgaggagt-tgcataacaattaaaaataaataaatgttgttattgac---catgtattat-tatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
                                                                                           | ||   || | |  | | |     || ||  |   |  |   |||| | | |       ||| |    ||   | ||   || |  |  || |         ||||  | ||||| || ||||| ||||| ||||| ||||||||  |||||||||| |||||||||||||| |||||||| || ||||| |||||| | || |
gtaagttctaggttaatacataattgaattgcatttctagctttccttttgtagttttgctttactcaattaaatcttgatttattagggatcatcatgtaatttcaggttcccttgtatgttttggatgtgccaatataaatactgctccattaaaatacacaaactaaacatctgatcatacacttttcgaaagGATGCTATGGCGCGGAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
-tgattgag---tcagtctaagctgaggagttgcataa-caattaaaaataaataaatgttgttattgaccatgtattattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
   |||||    |   | |||  | | |  ||  |||| ||||| |       ||  | || |  ||  || ||||| ||| |   | || | ||  | | |||||| |||||||  ||||||||||| ||||| || |||||||| ||||||||||| |||||||| ||||| ||||||||||| |||||||| ||| | ||||
cctattgacatttttttttaaaattatgccttaaataagcaatttagttccccta--tattatggtt--ccttgtatgattgttgatctgaa-attgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG

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|298194073|gb|HO040721.1|HO040721
EST:     CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
genomic: CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagttgct ... cccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
EST: gi|13312451|gb|BG406102.1|BG406102
EST:     CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
genomic: CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagttgct ... cccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
EST: gi|9564156|gb|BE473665.1|BE473665
EST:     CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
genomic: CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagttgct ... cccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
EST: gi|209705823|gb|BW675928.1|BW675928
EST:     CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
genomic: CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagttgct ... cccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG
EST: gi|151401960|gb|EV271773.1|EV271773
EST:     CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGACGGATG
genomic: CATCTGATGGTGCCCCTACTATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagttgct ... cccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataaatgttgttattgaccatgtattattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
             tattgac  putative branch site (score: 2)
                                            tcccgtctc  putative PPT
            ttattgaccatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgattgagtcagtctaagctgaggagttgcataacaattaaaaataaataaatgttgttattgaccatgtattattatatttttgtatatcccgtctcagGACACAATGGCTCGAAGACCTGCTGACCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - -gctgagg
- - - - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatgta