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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG

Basic information

species Glycine max
transcript GLYMA14G04890.1
intron # 30
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgat-----agAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG
            |   |   |||      |  |  |      |  |  || ||  || | || | || |||    |   |||  || ||||      |||||||| ||||     ||||||||||||||||||| |||||||| || || ||||||||||| ||||||||||   | || ||||| || ||| | |  || |||
----------gcaagttataattttaacatgctaggaagctaggcatgtccat--atgtgtacctccttttcttgaccgctg--ttcatgcc-atgatgtatcttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 26
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG
||| |||  | | |  |     | |    || | | ||| |||   ||  | ||| | | |   |  |||| || |        ||| || |   |||   ||||     ||||||||||||| ||||| || ||||||||||||||||| ||||||||| |||| | ||| || |||||  | ||  | |  || |||
gtaaattattgtttgttcc--ctacaggcttctctagtt-gtgcccataaatttgttgtgttctatgatttacaaa------gttttctgttctgatt---tctt----cagAGGAGAGATGTCTATGGAGCCTGGGAGCAGTATCTTGGTTTGGAGCATGCTGATACTGCACCAAAAAGGGCCTACACAGCCAATCAG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30
lower sequence: GRMZM2G014805_T02 (Zea mays), 3'ss of exon 11
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaattt-atgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG
                            | |  ||   || | ||| || |||  |||  |     ||||  | ||  |    |  | ||||||    | | | || | | ||||||||||||| |||||||||||||| || || |||||||||||||| || || |   |  | ||||| || ||  | |  || |||
-------------------------gcatgtgatttccttatcatacttaaatgcataccttctctcattcac-tacattcatacatgatgctt-tgctttttattat-acagAGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACCGATACAACATCGAAAAGGTCTTACACAGCCAATCAG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG
                              |  ||  ||    ||  || |||  |||  |       ||  | |   ||  |  | ||||||    | | | || | | || |||||||||| |||||||||||||| || || |||||||||||||| ||||| |   |  | ||| | || ||  |    || |||
-------------------------gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctt-tgctttttattat-acagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG

upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 30
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgctt--gcattgtatcttgtga-tagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG
                      |    | | |||  || | ||| |    | | |  ||||      ||||   ||| | |   |||||  ||  | |   |  ||||  |  |||| |||||||||||||||||||||||||||||||||||  | |||||| |||||| ||||||||||||  | ||||| | ||| |||
---------------------gtgtggtgtgtttgtgtgtatgaaatcatattgggcatttgcttttatttatttatttttatttttatttttttgaacattcacttgcaaacagAGAAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGACTAGAGCATTCTGACACTGCTCCTAAAAGGGCTTATGCAGCTAATCAG

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|21677323|gb|BQ629674.1|BQ629674
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
EST: gi|27427525|gb|CA939045.1|CA939045
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
EST: gi|5770494|gb|AI973668.1|AI973668
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
EST: gi|9565141|gb|BE474641.1|BE474641
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
EST: gi|58020429|gb|CX707171.1|CX707171
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
EST: gi|22523119|gb|BU081930.1|BU081930
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
EST: gi|207784911|gb|GD758228.1|GD758228
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
EST: gi|7283882|gb|AW596484.1|AW596484
EST:     GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAG                         AGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT
genomic: GGCGTCCTGAATATCTTCAGGATTCTGACATTGTATCCAGTCGTTTTCAGgtacattcat ... cttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG
          attttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT