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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatatatttttttcacatttttcccctaaagattattagtttttcagttgttcttgaacaatgaccatttaactatgttgcatacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAATGCACTTGAAACCTTGGCGGTAGGGACAACGGAAGAGAATGAG

Basic information

species Glycine max
transcript GLYMA08G01800.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 8
gtaaaaatatatttttttcacatttttcccctaaagattattagtttttcagttgttcttgaacaatgaccatttaactatgttgcatacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAATGCACTTGAAACCTTGGCGGTAGGGACAACGGAAGAGAATGAG
     || ||  ||     | || ||    ||||  |||     || ||||  ||||||| |  |||| |  || |   ||||||||| ||   |||||||| ||||||  ||||||||||| |  ||||||||| |||||||||  | |||||||||| | ||    ||||| || ||||| |||  |
---gtaagatgcttcaaata-atattctgtctaacaatt-----ttgttca-ctgttcttta--aatgtc--ttca---atgttgcatgcc-acagCAAAACAATCTTTATAAGGCTCGTGAAGAGAAGTATCAATCAAGAATAAGAGTACTTGAAACCCTTGCAACTGGGACCACTGAAGAAAATAGG
















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|207782310|gb|GD752845.1|GD752845
EST:     GCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAAAT                         CAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAA
genomic: GCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATG-AAAAATgtaaaaatat ... atacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAA
EST: gi|193406321|gb|FK373516.1|FK373516
EST:     TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAAT                         CAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTAT
genomic: TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAATgtaaaaatat ... atacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTAT
EST: gi|208298630|gb|GE094153.1|GE094153
EST:     TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAACATGAAAAAT                         CAAAACAATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAAT
genomic: TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAATgtaaaaatat ... atacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAAT
EST: gi|208194248|gb|GD994335.1|GD994335
EST:     TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAAT                         CAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAAT
genomic: TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAATgtaaaaatat ... atacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAAT
EST: gi|207811204|gb|GD783041.1|GD783041
EST:     TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAAT                         CAAAACCATCTTTTCAAGG
genomic: TGCAAGTAATTCAGTTGCGCTTTTCAAATCAAGCAGAAAGCATGAAAAATgtaaaaatat ... atacctgaagCAAAACCATCTTTTCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtttttcagttgttcttgaacaatgaccatttaactatgttgcatacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAATGCACTTGAAACCTTGGCGGTAGGGACAACGGAAGAGAATGAG
                              atttaac  putative branch site (score: 3)
                              atttaactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatatatttttttcacatttttcccctaaagattattagtttttcagttgttcttgaacaatgaccatttaactatgttgcatacctgaagCAAAACCATCTTTTCAAGGCTCGTGAGGGAAAGTATCAAACAAGAATAAATGCACTTGAAACCTTGGCGGTAGGGACAACGGAAGAGAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA