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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtattgttaaattgtatttgtccattgattaattatttttgttattatgtgacaatttccgtattcatttataatttcttctttagGATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAAGACATCTTCAGCGTGAAAGATTTACCTGCTTACAACATGTTGAGATGAT

Basic information

species Glycine max
transcript GLYMA19G29990.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G29990.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0056g00790.t01 (Vitis vinifera), 3'ss of exon 9
--gtaatgtattgttaaattgtatttgtccattgattaattattttt----gttattatgtgacaatttccgtattc---atttataatttcttctttagGATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAAGACATCTTCAGCGTGAAAGATTTACCTGCTTACAACATGTTGAGATGAT
  |  |   ||||  ||    | || |     | |  ||   |||||       ||  |   | |  | |  |||||   ||||    | | |||  ||||||||| | |  || || ||||| ||  ||||||| |||||||  ||||||||  ||||||| |||| ||||||||| || ||||||||||||||| |||
ttgccagcaattgagaaccatttttagagttgtcaaaaaccgttttttgaaaacatcgtcgaatagatgctttattctccattttggttgttttccgtagGATGTTCTAAAGTCTACCAGAACACAACTAGAGCGGGAGCTTGAGCTTGAAGATGTCTTCAGTGTGAGAGATTTACCAGCATACAACATGTTGAGAAGAT
















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|6134331|gb|AW132724.1|AW132724
EST:     TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAAATTAAT                         GATGTNTTTG-GATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGA
genomic: TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAATTTAATgtaatgtatt ... tcttctttagGATGT-TTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGA
EST: gi|22523888|gb|BU082699.1|BU082699
EST:     TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAATTTAAT                         GATGTTTTGAGATCCACAA
genomic: TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAATTTAATgtaatgtatt ... tcttctttagGATGTTTTGAGATCCACAA
EST: gi|27423797|gb|CA935317.1|CA935317
EST:     TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAATTTAAT                         GATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAA
genomic: TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAATTTAATgtaatgtatt ... tcttctttagGATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAA
EST: gi|58017180|gb|CX703922.1|CX703922
EST:     TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAATTTAAT                         GATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAA
genomic: TGATGGATGCTCAGTGGCTAGCAAAGCGTGCGTCATATATGGAATTTAATgtaatgtatt ... tcttctttagGATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatttttgttattatgtgacaatttccgtattcatttataatttcttctttagGATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAAGACATCTTCAGCGTGAAAGATTTACCTGCTTACAACATGTTGAGATGAT
 gattaat  putative branch site (score: 3)
                                           tttcttcttt  putative PPT
                              tattcatttataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtattgttaaattgtatttgtccattgattaattatttttgttattatgtgacaatttccgtattcatttataatttcttctttagGATGTTTTGAGATCCACAAGAACGCAGTTAGAGCGTGAGCTTGGTCTTGAAGACATCTTCAGCGTGAAAGATTTACCTGCTTACAACATGTTGAGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG