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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgttgatcttctgaagctttactcagtaaggaacagctataatcatttttactttttgaaggggtacaaaactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCTGCTGCCATTGATGGGCTTCCAGATCCTGGTGGGCCAACAGT

Basic information

species Glycine max
transcript GLYMA20G37520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37520.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0128g00050.t01 (Vitis vinifera), 3'ss of exon 2
cttgttgatcttc-tgaagctttactcagtaaggaacagctataa-tcatttttactttttgaag----gggtacaaaactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCTGCTGCCATTGATGGGCTTCCAGATCCTGGTGGGCCAACAGT
      |||  || |    ||| | |   ||| ||| |||  ||| |  |  | |    |||||     ||  |    | ||  |   | ||||| |    |||||| || || || || || ||||||||||||||  |||| |||| ||| ||||||||||  |||||||||||||| ||||||||| ||||||| ||| ||||
------gattctcatttttcttgatttgataatgaatagcagtaaattttcctcagcaattgaattcatggtaattggagtatttgattttggttgactactgcagTTTTAGCAACTGAAGAAAAGTACAATGAAGCAGTTTTCAGCAGTGCCAAACGGCTAGTGGCTGCCATTGATGGCCTTCCAGATGCTGGTGGCCCATCAGT
















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|192296100|gb|FG989460.1|FG989460
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTG                         T-TTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|193326943|gb|FK287826.1|FK287826
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|6134161|gb|AW132554.1|AW132554
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTG                         TATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAAC
EST: gi|11413879|gb|BF425890.1|BF425890
EST:     AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTG                         TATTGGCTACGGATGAGAAG
genomic: AGCTGTGGGGGAAAAGATCCTTGATGCTACCGTCTCAGAGAACCTTCCTGgtacttgcaa ... atatatgcagTATTGGCTACGGATGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttactttttgaaggggtacaaaactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCTGCTGCCATTGATGGGCTTCCAGATCCTGGTGGGCCAACAGT
                                          tttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgttgatcttctgaagctttactcagtaaggaacagctataatcatttttactttttgaaggggtacaaaactacctatgtctggtttatatatgcagTATTGGCTACGGATGAGAAGTACAATGAAGCTATTTTTAGCACTGCTAAACGGCTAGCTGCTGCCATTGATGGGCTTCCAGATCCTGGTGGGCCAACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
cttgttg
- - - - tcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatgtc