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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggtgagaaagaatagctatcctgcatcagcaattcccatgaaaaattgttgtgataagcagcttttgacaatttccgtaaattcatgtctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCCCAATGCTGCTGAAAGATTTGGAATATCTCTAAGTG

Basic information

species Glycine max
transcript GLYMA17G26900.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G26900.3 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g03260.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------------------------------tttggtgagaaagaatagctatcctgcatcagcaattcccatgaaaaattgttgtgataagcagcttttgacaatttccgtaaattca--tgtctcct----gcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCCCAATGCTGCTGAAAGATTTGGAATATCTCTAAGTG
                                                                                 |||| || ||      |  |||  | |  |   | ||   ||  ||  |  || || |       ||| |    | |  |||| |||   ||| ||      |||| || |||| |||||||||||| |||||||||||||||||||| ||||| || ||||  || |||| ||||||||||||| |  |||
gtatgtttcttgcttcagtaacctgagctaaaatgaaaactttcagcaacttgcatcagttgtgaaatcaaccccattgtatttgttgtgactcttcacttatttt-ctccttaattttttattgaagttccttttgct---tgattttaggtggtgttagtaatttctcctgtttctgtttagcagTTACTCAAACAAAAATTTATCTTTTGGAATAGTTGATCTTGGCCTCTTCCCAAATGTGGCAGAAAAATTTGGAATATCTGTTGGTG
















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|151401073|gb|EV270887.1|EV270887
EST:     TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
EST: gi|151412705|gb|EV282517.1|EV282517
EST:     TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
EST: gi|151396592|gb|EV266469.1|EV266469
EST:     TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
EST: gi|254342909|gb|GR859071.1|GR859071
EST:     TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
EST: gi|6719570|gb|AW307217.1|AW307217
EST:     AGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: AGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
EST: gi|15203897|gb|BI426665.1|BI426665
EST:     TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
EST: gi|151402880|gb|EV272693.1|EV272693
EST:     TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
EST: gi|254342910|gb|GR859072.1|GR859072
EST:     TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTAC                         ATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC
genomic: TCACCTGCTTGCATTCGCTCAAGTCAGCAGTTTCCTGAGCTCTCAATTACgtatgcttct ... tctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattgttgtgataagcagcttttgacaatttccgtaaattcatgtctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCCCAATGCTGCTGAAAGATTTGGAATATCTCTAAGTG
                    ttttgac  putative branch site (score: 3)
                                           tgtctcct  putative PPT
                                   taaattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggtgagaaagaatagctatcctgcatcagcaattcccatgaaaaattgttgtgataagcagcttttgacaatttccgtaaattcatgtctcctgcagATATTCAAGCAAAAATTTATCATTTGGAATAGTTGATCTTGGTCTCTTTCCCAATGCTGCTGAAAGATTTGGAATATCTCTAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT