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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaataagattgagatcctatatcactaacaattaaggcttagtaatcttagcaagttctgattacaacaagggtattttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA

Basic information

species Glycine max
transcript GLYMA10G32500.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 11
gtaaaaataagattgagatcctatatcactaacaattaaggcttagtaatcttagcaagttctgattacaacaagggtattttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA
|| |  | ||  |   |   | |||   |    |||| |   ||| | |||| |  ||   |   ||  | ||    | |||  || ||||||||||  |||||| ||| || ||||||||||| || ||||||||||||||||||||  | ||||||||||||||||||||||||   |||||||  |
gtgatcacaacttcttg---ccataaagcagtgaattcactgttaatcatctaaataa---caagttggatcatc--tttttatttcagGAACGTGAAAATCCAACTTTAACCGAGTGGGATCGGTTCGCACATAGAGAGTATATTAGATTGTCCATGGAAGAAGATGGTGAAGATGCTTCAAATGGAA

upper sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 11
gtaaaaataagattgagatcctatatcactaacaattaaggcttagtaatcttagcaagttctgattacaacaa-----gggtattttgtt-tagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA
              | |||  || |||  |||    |||   ||||   |  |  |||||  | | |  || ||        | |||  || |||||||||||  |||||| | | || |||||||| || |||||||||||||| ||||||||  | |||||||||||||||||||| |||   |||||||  |
--------------gtgattata-atccttaa----taaactttagatttgctgccaagtattaagttaaataattggctaatgtttaattgtagGAACGTGAAAATCCAACTCTAACTGAGTGGGACCGGTTTGCACATAGAGAATATATTAGATTGTCCATGGAAGAAGATGGTGAGGATGCTTCAAATGGAA
















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|9204760|gb|BE330984.1|BE330984
EST:     TCAACAAGTTTATTGCTTTCGAGACTCGTGATCCATTTCTCATACGTCAG                         TAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAG
genomic: TCAACAAGTTTATTGCTTTCGAGACTCGTGATCCATTTCTCATACGTCAGgtaaaaataa ... ttttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAG
EST: gi|21256450|gb|BQ453338.1|BQ453338
EST:     TCAACAAGTTTATTGCTTTCGAGACTCGTGATCCATTTCTCATACGTCAG                         GAACGTGAGGATCCAAATTTGACTGAGTGGGATCGTTTTGCACATAGAGAG
genomic: TCAACAAGTTTATTGCTTTCGAGACTCGTGATCCATTTCTCATACGTCAGgtaaaaataa ... ttttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaggcttagtaatcttagcaagttctgattacaacaagggtattttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA
                         ttctgat  putative branch site (score: 3)
                                             ttttgttt  putative PPT
                                           tattttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaataagattgagatcctatatcactaacaattaaggcttagtaatcttagcaagttctgattacaacaagggtattttgtttagGAACGTGAGGATCCAAATTTGACAGAGTGGGATCGTTTTGCACATAGAGAGTATATTAGGCTTTCCATGGAAGAAGATGGTGAAGATATGTCAAATGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA