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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttaccctaaaagtttgcaatttaagttctcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT

Basic information

species Glycine max
transcript GLYMA09G39800.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os04g58580.1 (Oryza sativa), 3'ss of exon 7
gttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttaccctaaaagtttgc-aatttaagttct-cagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT
                         | |     | | || || |     | | |  |||||    |    |   ||| | ||| ||  |  | |||  | ||  |||| || ||||| || || |||||||| || || |||||||| ||||| || ||  | ||||||||||| || |||||||| ||||| |||||||||
------------------------gtacaaacaattctttacaaagagcaataatttgttatcattcaggc---accatgaaacttaactgacttatttactatagGTACATAACATTCGGCCTAAAATGGTCTCAGTGCTTCGTGAAAAGTTCGCCCACTTGAACTTGACATTTTCTATTGGAGGGCAGATTAGTTTTGAT

upper sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 8
gttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttaccctaaaagtttgcaatttaagttct--cagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT
             || |  ||  | | ||  |      |  || | | || |   |    | |     || | ||   |   | |     | || | |||   ||||| || ||||| || || |||||||| || || |||||||| |||||||| ||  | ||||||||||| || || ||||| ||||| |||||||||
-------------gtataaattgtgtactaaaagtcagtaccttttcttagtaggagaggatggaataaaatcta---tgggactgaaacagttgatttcctgcagGTGCATAACATCCGACCTAAAATGGTGTCAGTGCTTCGTGAAAAGTTTGCACACATGAACTTGACATTTTCTATCGGAGGGCAGATTAGTTTTGAT

upper sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 8
lower sequence: AT2G45790.1 (Arabidopsis thaliana), 3'ss of exon 6
gttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttaccctaaaagtttgcaatttaagttctcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT
                |  |  | | | | |  | |||   | ||   |  |  ||| |    ||   |   | |  | | |  |||    |||||      ||||||| ||||| || ||||| |||||  ||| ||||||||||  |||||| ||||||||| | || ||||| ||||| ||||||||||| || |||
---------------gtagaagaaactatatttagtttgttcaatttcttatagaatatattttgagcattgtcattcaacactttt----tttaaa-----agGTTCAAAACATCCGACCAAAGATGGTAGCTGAACTTCGTGAGCGGTTTGCACATCTTAACCTTACTTTCTCAATTGGGGGACAGATAAGCTTCGAT

upper sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 7
gttatgtattttggtttttatca--tattctctagaattttcact----atccatattgaaatgttaggtgtat-------aactt-taccctaaaagtt----tgcaatttaagttc---tcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT
  |||  | ||  | |  |   |   |     | ||| | ||| |     |   |    | |  ||   |||||       ||| |  | ||| |||         |||||||   ||   |||| ||||||||||||| || || ||||||||||| |||||||||||||||||||| || ||| ||||||| || ||||||||||| ||||| ||||||
-gtataaacttcagatccttcgaagcaaaagattgaactgtcaatttgtgtttgtggcaataaattgattgtatttggataaacatgcatcctgaaacaaacaacacaatttataatcatatcagATTCACAACATACGTCCGAAGATGGTTTCTGTGCTTCGTGAGAAGTTTGCTCACCTAAACCTGACATTTTCTATTGGAGGACAAATAAGCTTTGAT

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|151397333|gb|EV267206.1|EV267206
EST:     GCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAG                         GTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCT
genomic: GCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAGgttatgtatt ... aagttctcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCT
EST: gi|151394604|gb|EV264475.1|EV264475
EST:     GCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAG                         GTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCT
genomic: GCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAGgttatgtatt ... aagttctcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCT
EST: gi|192301212|gb|FG988977.1|FG988977
EST:     GCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAG                         GTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCT
genomic: GCCGAAACTGTAGCCAAGAAGAAAGAGATGAGTTTGAGAAATATGACAAGgttatgtatt ... aagttctcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaaatgttaggtgtataactttaccctaaaagtttgcaatttaagttctcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT
                          ccctaaa  putative branch site (score: 3)
                                                ttctc  putative PPT
                tataacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatgtattttggtttttatcatattctctagaattttcactatccatattgaaatgttaggtgtataactttaccctaaaagtttgcaatttaagttctcagGTTCACAACATACGCCCAAAAATGGTTTCTGTACTTCGTGAGAAGTTTGCTCATCTTAACTTGACATTCTCCATTGGAGGACAGATAAGTTTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA