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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttagacatatgaattagtagtatatgatattatatacacacatacatatacttttctgggcatgatcgagtctctatatatatatacccatacatttactttggttaatttaaacatgtgaacattgtttgttttagGAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAGATAAATAATTGGTTCATAAATCAAAGGAAAAGGAACTGGCATACAAATA

Basic information

species Glycine max
transcript GLYMA17G11330.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11330.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0118g00800.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtttagacatatgaattagtagtatatgatattatatacacacatacatatacttttctgggcatgatcgagtctctatatatatatacccatacatttactttggttaatttaaacatgtgaacattgtttgttttagGAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAGATAAATAATTGGTTCATAAATCAAAGGAAAAGGAACTGGCATACAAATA
                            | || || |  ||   |   |   | |  |||      || ||  | |||| | | | |  | || | ||||    |     ||  |||||| ||            ||||||||||||||||||| ||  || |||||||||||||||| ||||| ||||||||||| ||||| |||||||| || ||||||||| |||| ||||| |  ||| 
---------------------------gtgtgttacttaatcttcttttggctgtcattt----aacacga--gggtctttttcttttgaaactc-tacaaactccc-atttgctttaaatat------------tgttttagGAGGAAGACAAAGCACGACTGGTGCAGGAAACAGGCTTGCATTTAAAGCAGATCAATAACTGGTTCATCAACCAAAGGAAACGGAATTGGCACAGCAATC
















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|254341374|gb|GR855102.1|GR855102
EST:     CCCTTTTGAAAGCTTGGTGGCAATCACATTCTAAATGGCCTTACCCCACT                         GAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAG
genomic: CCCTTTTGAAAGCTTGGTGGCAATCACATTCTAAATGGCCTTACCCCACTgtaagtttag ... tttgttttagGAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAG
EST: gi|17153712|gb|BM143645.1|BM143645
EST:     CCCTTTTGAAAGCTTGGTGGCAATCACATTCTAAATGGCCTTACCCCACT                         GAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAG
genomic: CCCTTTTGAAAGCTTGGTGGCAATCACATTCTAAATGGCCTTACCCCACTgtaagtttag ... tttgttttagGAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAG
EST: gi|15287510|gb|BI471401.1|BI471401
EST:     CCCTTTTGAAAGCTTGGTGGCAATCACATTCTAAATGGCCTTACCCCACT                         GAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAG
genomic: CCCTTTTGAAAGCTTGGTGGCAATCACATTCTAAATGGCCTTACCCCACTgtaagtttag ... tttgttttagGAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacccatacatttactttggttaatttaaacatgtgaacattgtttgttttagGAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAGATAAATAATTGGTTCATAAATCAAAGGAAAAGGAACTGGCATACAAATA
                    ggttaat  putative branch site (score: 4)
                                             tttgtttt  putative PPT
           atttactttggttaat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttagacatatgaattagtagtatatgatattatatacacacatacatatacttttctgggcatgatcgagtctctatatatatatacccatacatttactttggttaatttaaacatgtgaacattgtttgttttagGAGGAAGACAAGGCTAGATTGGTGCAGGAAACAGGGTTGCAATTAAAGCAGATAAATAATTGGTTCATAAATCAAAGGAAAAGGAACTGGCATACAAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA