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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcattcttctcttcctcgtacttactttaccgtgtttctataactgactgtgaattctaacaactaacattggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTTTTGGCGGGGCAGAGGCAATTGTTGAAGACGATAAAGAGGAGGAGGCACG

Basic information

species Glycine max
transcript GLYMA04G05500.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G05500.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g01110.t01 (Vitis vinifera), 3'ss of exon 1
----------------gtaagcatcattcttctcttcctcgtacttactttaccgtgtttctataactgactgtgaattctaacaactaacattggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTTTTGGCGGGGCAGAGGCAATTGTTGAAGACGATAAAGAGGAGGAGGCACG
                 | ||     ||  | | ||  |  ||  |      |  |  | || | | |     ||   | | |    |   || | ||||||||||||||||| | ||||| ||    ||||||||||| || |||||||||||||  ||||||| |||  || ||||||  || ||||| || || || |
ttgattctagtttatattgagttaatttgattttttttttataagtttcaatctttactgctttgattc-tgatgggctttgatgcttgcaatggatgcagGGTTTTAGAAAAGTCGATCCAGATCGATGGGAGTTTGCAAATGAAGGGTTTTTGGGAGGGCAGAAGCATCTGCTGAAGAACATCAAGAGAAGAAGACATG
















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|18692806|gb|BM521654.1|BM521654
EST:     ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTAC                         GGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
genomic: ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTACgtaagcatca ... attggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
EST: gi|16996721|gb|BM086093.1|BM086093
EST:     ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTAC                         GGTTTTAGAAAAATTGATCCTGACAAGTGNNNNNNNGCGAACGAAGGGTTT
genomic: ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTACgtaagcatca ... attggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
EST: gi|209705786|gb|BW661454.1|BW661454
EST:     ACTTCGAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTAC                         GGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
genomic: ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTACgtaagcatca ... attggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
EST: gi|213601427|gb|DB968729.1|DB968729
EST:     ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTAC                         GGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
genomic: ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTACgtaagcatca ... attggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
EST: gi|6341760|gb|AW164509.1|AW164509
EST:     ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTAC                         GGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT
genomic: ACTTCAAGCACAACAATTTCTCCAGCTTCGTACGACAACTCAACACCTACgtaagcatca ... attggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actttaccgtgtttctataactgactgtgaattctaacaactaacattggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTTTTGGCGGGGCAGAGGCAATTGTTGAAGACGATAAAGAGGAGGAGGCACG
                                      aactaac  putative branch site (score: 1)
           tttctataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatcattcttctcttcctcgtacttactttaccgtgtttctataactgactgtgaattctaacaactaacattggtgcagGGTTTTAGAAAAATTGATCCTGACAAGTGGGAGTTTGCGAACGAAGGGTTTTTGGCGGGGCAGAGGCAATTGTTGAAGACGATAAAGAGGAGGAGGCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG