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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgtttaattatttctgaaatggttaatcaatatggtgtatgcatgataattatcacttatgcaaattttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAACCAGCAATGGCAGTGCCTCCTATGCAGCAGATGTCACGCATTGATCAAC

Basic information

species Glycine max
transcript GLYMA08G01990.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01990.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g39100.1 (Oryza sativa), 3'ss of exon 7
------gtaagtttgtttaattatttctgaaatggttaat--caatatggtgtatgcatgataa-ttatcactta--tgcaaattttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAACCAGCAATGGCAGTGCCTCCTATGCAGCAGATGTCACGCATTGATCAAC---------
      | |  ||| |||  ||| ||      ||  ||||  || |    |  || | |||||  |||| |   |  |||||| | |   | ||||| ||||||||| | |||||||||||| | ||||| || ||||||||          ||| |||||||||| |||||||||||||| ||||| |||||||         
gtaatggcacatttttttttttactttcctcctgaataatctcactgctttaaattcctgatatcttatgatgaaactgcaaaatgtaaattcagACACAGCACAAGGTCGAGATGGACAAGAGGGACGGCAAGTTTGGACCT---------ATGACAGTGCCTCCAATGCAGCAGATGTCTCGCATCGATCAACCGGTTCCGC

upper sequence: GLYMA08G01990.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g03180.1 (Oryza sativa), 3'ss of exon 7
gtaagtttgtttaattatttctgaaatggttaatcaatatggtgtatgcatgataattatcacttatgca---aattttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAACCAGCAATGGCAGTGCCTCCTATGCAGCAGATGTCACGCATTGATCAAC---
||||   |   ||||   ||  |  ||  || |   |       ||  | |      |    ||||| ||   || |   | ||||||| || ||||| ||||| ||||||||| |||| ||||| || || || || ||    |||||||||||||| |||||||| ||||| ||||| ||||| |   
gtaaacatacataatatctttggtgattatttactcactcttcttaacctttgcgtatccatcttatccactgaaatgcatgtgcagACCCAACACAAAATTGAAATGGACAAGAGAGATGGGAAGTTCGGCCCACAGCCC---ATGGCAGTGCCTCCAATGCAGCAAATGTCGCGCATCGATCAGCCTA

upper sequence: GLYMA08G01990.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv02s0025g00130.t01 (Vitis vinifera), 3'ss of exon 7
------------------------gtaagtttgtttaattatttctgaaatggttaatcaatatggtgtatgcatgataattatcacttatgcaaattttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAACCAGCAATGGCAGTGCCTCCTATGCAGCAGATGTCACGCATTGATCAAC---
                         |     ||   ||   | |||   ||   |||  |  | |    |   ||| ||| |     |  ||   | |    |||||||| || ||||||||||| |||||||||||||| || |  |||||||| |||||    |||||  | || ||| ||||||||||||||||||||||||| |   
gtaagcaagagctacaacaaacacatgcaaatgagaaaccgtatct---atatctaaatatcacgtcacac-tatgttaactgatgttcttgtggagt---attgcagACCCAACACAAGATTGAAATGGACAAGCGAGATGGCATGTTTGGACCACAACCC---ATGGCCATACCCCCTTTGCAGCAGATGTCACGCATTGATCAGCCAT

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|207800546|gb|GD774585.1|GD774585
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|23732520|gb|BU764420.1|BU764420
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|254328214|gb|GR835179.1|GR835179
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|192308244|gb|FK002756.1|FK002756
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|13312651|gb|BG406302.1|BG406302
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|31461793|gb|CD403821.1|CD403821
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|192299321|gb|FG992499.1|FG992499
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|16105268|gb|BI893008.1|BI893008
EST:     CTGCACGGTCTGTGCATGTATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|209703865|gb|BW656915.1|BW656915
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
EST: gi|192302560|gb|FG996296.1|FG996296
EST:     CTGCACGGTCTGTGCATGCATGCAG                         ACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA
genomic: CTGCACGGTCTGTGCATGCATGCAGgtaagtttgt ... ttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatcaatatggtgtatgcatgataattatcacttatgcaaattttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAACCAGCAATGGCAGTGCCTCCTATGCAGCAGATGTCACGCATTGATCAAC
 ggttaat  putative branch site (score: 4)
                                           ttttgttt  putative PPT
                       ataattatcacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgtttaattatttctgaaatggttaatcaatatggtgtatgcatgataattatcacttatgcaaattttgtttgcagACTCAGCACAAGATTGAGATGGACAAGCGAGACGGGAAATTTGGACCCCAACCAGCAATGGCAGTGCCTCCTATGCAGCAGATGTCACGCATTGATCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG