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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agccattactgtggcctatgcggaagttttgattatcagtttcttctcctaattattcttgtttatttggttttaccactttgcccaatgttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGTCTTAAGTGAACTCTCATGCCCGTTGTTGCTGCTTTGGGGTGACCTTGAC

Basic information

species Glycine max
transcript GLYMA16G25200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25200.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g02010.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------------------------------------------agccattactgtggcctatgcggaagttttgattatcagtttcttctcctaattattct----tgtttatttggttttaccactttgcccaatgttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGTCTTAAGTGAACTCTCATGCCCGTTGTTGCTGCTTTGGGGTGACCTTGAC
                                                                                    ||  | |  | | | | ||| ||  |||||  |  |   | | |    || | |  | |      ||   ||| || |    || | | |  |||| ||||||| |||||||| || |||||||||||||| ||||||||||| ||  |   |||||||||  ||||||| |||||| ||||| |||| ||||||||| | || 
gtatggatgtgaatgtgttcctccattctatcacagtatgaacaggggctccatggctttaaaagtcgcataaatctttggtttagaaacttgt-taggccatgtggg-gttttcttcctttctctgtgaaactgaatgctatatacccttcccttgcttatgatgctgtcctctctgttttctacagATTAATGACCCGGTTCATGATGAATCAAAGCAAGTACACCCTTAACAGTGTCTTAAGCAAACTCTCTTGCCCGCTGTTGTTGCTCTGGGGTGACTTAGAT
















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|192301617|gb|FG998469.1|FG998469
EST:     TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTTTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
EST: gi|197666163|gb|FD480429.1|FD480429
EST:     TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTTTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTAC
genomic: TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTAC
EST: gi|213604005|gb|DB974187.1|DB974187
EST:     CTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGCAC-ACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: CTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAG-TCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
EST: gi|298173858|gb|HO017194.1|HO017194
EST:     TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTTTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
EST: gi|51337924|gb|CO981790.1|CO981790
EST:     TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTTTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
EST: gi|209728318|gb|BW658530.1|BW658530
EST:     TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
EST: gi|209716248|gb|BW657551.1|BW657551
EST:     CGGAGAAGTTTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: CGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
EST: gi|151405996|gb|EV275811.1|EV275811
EST:     TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
EST: gi|151405769|gb|EV275583.1|EV275583
EST:     TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAG                         GTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT
genomic: TCTATAACAAGGCCAGCTCAAGATCCAAATGCCGGAGAAGTCTACTACAGgtacatgacc ... ttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcctaattattcttgtttatttggttttaccactttgcccaatgttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGTCTTAAGTGAACTCTCATGCCCGTTGTTGCTGCTTTGGGGTGACCTTGAC
 tcctaat  putative branch site (score: 2)
     aattattcttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agccattactgtggcctatgcggaagttttgattatcagtttcttctcctaattattcttgtttatttggttttaccactttgcccaatgttgtctacagGTTAATGACGCGCTTCATGATGAATCAGAGCAAGTACACTCTAGATGCTGTCTTAAGTGAACTCTCATGCCCGTTGTTGCTGCTTTGGGGTGACCTTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
agccatt
- - - -actgtgg
- - - - - - - cctatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttgcc