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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataattagttgttttattttctttttattcaccacagtgcttctgattgtgcctgtttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC

Basic information

species Glycine max
transcript GLYMA11G03590.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os06g01650.1 (Oryza sativa), 3'ss of exon 11
--------------gtataattagtt--gttttattttctttttattcaccacagt-gcttctgattgtgcctgtttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC
               |  ||||  |    |     ||||    |      |||||| | || |||||          || |  ||||| || | | ||| |    ||| ||  |||| ||  ||||||||||||| ||||| |||||||||||| | |||||||| |||||||||||  | || ||||| ||  || |   ||  |
gtgcttgctaaaacattaaattcatccgatcccggtttcgaactgcatgtcacagtagtttttgatttgtgtaacacaactaattctt-ttgtgccctaaa----gGCGAAGCTGGGGGAACAAAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTGGAAGAAGGTGCTGACATACCTGCTGAGGAGCCTCCCCTTCCCC

upper sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os02g01490.1 (Oryza sativa), 3'ss of exon 11
gtataattagttgttttattttctttttatt-caccacagtgcttctgattgtgcctgtttaaatggttcttattcta-----ctctatatgt-----agGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC
|||   |||  ||   ||||   ||       | ||||  |  ||| | || |      |  | |    || || ||      ||   |||||     |||||||||| ||  |  |||||||||| || ||||| || ||||| ||| ||||||||||||||||||||||  |||| || || ||  || ||   |  |
gtact-ttaactgagctattgaattggagccactccacttttgttcagtttctcttccatatagtaaagctaatactgagatccttcctatgtcttgaagGCTAAATTAGGGCAACAAAACAAGTTTTACTATGACGAAAAGCTAAAGCGATGGGTGGAGGAAGGTGCTGAGATTCCTGCCGAGGAGCCTCCTCTCCCTC

upper sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G104958_T01 (Zea mays), 3'ss of exon 12
gta-taattagttgttttatttt--ctttttattcaccacagtgcttctgattgtgcctgtttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC
||| |  ||||    || | |      || | ||     |  ||||| || || | |    | | ||||||    | ||  | | | || |||| ||  | || ||  | ||||||||||| ||||| |||||||||||| | ||||| || |||||||||||  | || || || ||  |  |   ||  |
gtacttgttagcacattaagtacaatgttctgttgttgtctatgcttttggttctccgcagtaacatggttaccctcctgatat-tctgaagGCAAAGCTAGGGGAACAGAACAAGTTCTACTATGACGAGAAGCTGAAGCGGTGGGTTGAAGAAGGTGCTGAGATCCCTGCCGAGGAGCCCCCACTTCCCC

upper sequence: GLYMA11G03590.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv15s0021g02730.t01 (Vitis vinifera), 3'ss of exon 12
gtataattagttgttttattttcttttt-------attcaccaca-gtgcttctgattgtgcctgt--ttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC
   || ||  ||||  || ||  || |        | || |   |  |  |  |  || | |  ||  | ||||  ||  |  | |  |||   || |||| ||| | |||||||| || || || ||||||||||| ||||| ||| ||||||| ||||||||| ||||| ||||| ||||||||||  |    | ||
--gtagtttcttgtgctagttgtttctgtaaatagactccctgtatataatcatctttttactggtgatcaaatattttatgctatgttcttactgaagGCAAAACTAGGTGAGAAGAATAAATTTTATTATGATGAAAAGCTCAAGCGATGGGTTGAGGAAGGTACTGAACTTCCATCTGAAGAAGCAGCCTTGCCGC

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|192315142|gb|FK009966.1|FK009966
EST:     TTTTGCAAAAGACCGTAGGGCTAGTCTTGAAACCTCGCTCTGGTCGACAG                         GCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGA
genomic: TTTTGCAAAAGACCGTAGGGCTAGTCTTGAAACCTCGCTCTGGTCGACAGgtataattag ... ctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGA
EST: gi|192315141|gb|FK009965.1|FK009965
EST:     TTTTGCAAAAGACCGTAGGGCTAGTCTTGAAACCTCGCTCTGGTCGACAG                         GCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGA
genomic: TTTTGCAAAAGACCGTAGGGCTAGTCTTGAAACCTCGCTCTGGTCGACAGgtataattag ... ctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacagtgcttctgattgtgcctgtttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC
        ttctgat  putative branch site (score: 3)
                                ttcttattctactct  putative PPT
                     tgtttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataattagttgttttattttctttttattcaccacagtgcttctgattgtgcctgtttaaatggttcttattctactctatatgtagGCTAAATTGGGTGAGAAAAACAAGTTCTATTATGATGAGAAGCTGAAGAGATGGGTGGAGGAAGGTGCTGAAGTTCCAGCTGAAGAAGCTTCTGCTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC