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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttgatctatttcggtgttgtgaaactccttttcattgcaatttttcacttgtaactgaaaactcaacaaaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAGGGGGTGCTTGATCCCAAGCTTCCTGAGAAACCAACTTCAAGAGCACTAA

Basic information

species Glycine max
transcript GLYMA11G05830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0031g00480.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------gttagtttgatctatttcggtgttgtgaa--actccttttcat-tgcaatttttcac----ttgtaactgaaaactcaacaaaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAGGGGGTGCTTGATCCCAAGCTTCCTGAGAAACCAACTTCAAGAGCACTAA
                                 | |  |||  |    |    || ||   |     | |||| || |    | || | |     | | ||| | || |||    |||||||||||||| || || |||||||| |||| |||||||| || ||| ||||||||||| ||  | ||||| ||| | |||||||| || |||||||| ||  | |
gtatgccctaaactacttggatcgtttcttggtgatgatttagttatgtaaaatgctgaagattgtccttttttatgtttggtcttccccattgcttttactcacaaatcag--gaattttcagGTGAACTTAGTTGACTGGCTTAAGAGGATGGTTACCAGCAGGAATCCAGAGGGAGTTTTGGATCCAAAGATACCTGAGAAGCCGACTTCAAGGGCCTTGA
















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|213617268|gb|DB978950.1|DB978950
EST:     ACTAATTACAGGAAGGAATCCGGTTGA-TACTAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
genomic: ACTAATTACAGGAAGGAATCCGGTTGATTA-TAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
EST: gi|10234344|gb|BE803232.1|BE803232
EST:     AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
genomic: AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
EST: gi|207822203|gb|GD793564.1|GD793564
EST:     AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
genomic: AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
EST: gi|207791527|gb|GD763238.1|GD763238
EST:     AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAAGA
genomic: AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCA-GA
EST: gi|58016385|gb|CX703127.1|CX703127
EST:     AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
genomic: AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
EST: gi|207828657|gb|GD800502.1|GD800502
EST:     AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
genomic: AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
EST: gi|26048897|gb|CA785350.1|CA785350
EST:     AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
genomic: AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
EST: gi|207844892|gb|GD815259.1|GD815259
EST:     AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAG                         GTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG
genomic: AACTAATTACAGGAAGGAATCCGGTTGATTATAGTCGGCCTCCAGAAGAGgttagtttga ... aaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actccttttcattgcaatttttcacttgtaactgaaaactcaacaaaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAGGGGGTGCTTGATCCCAAGCTTCCTGAGAAACCAACTTCAAGAGCACTAA
                         ttgtaac  putative branch site (score: 2)
                                                ttttc  putative PPT
                                         aacaaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttgatctatttcggtgttgtgaaactccttttcattgcaatttttcacttgtaactgaaaactcaacaaaattttcagGTGAATTTGGTAGACTGGCTCAAGAAGATGGTTAGCAACAGAAATCCAGAGGGGGTGCTTGATCCCAAGCTTCCTGAGAAACCAACTTCAAGAGCACTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA