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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttgcatcaagattttaaattaacattgagtgagaatactggcaatttaattgatgagatttcttgagttatttttctaacaatttgtttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGGGCTATGTTGGCTCTCATTGATGCTGGACAG

Basic information

species Glycine max
transcript GLYMA01G00430.2
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G00430.2 (Glycine max), 3'ss of exon 16
lower sequence: Vv11s0065g00640.t01 (Vitis vinifera), 3'ss of exon 16
cttttgcatcaagattttaaa--ttaacattgagtgagaatactggcaatttaattgatgagatttcttgagttatttttctaacaattt---------gtttttgtt---cagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGGGCTATGTTGGCTCTCATTGATGCTGGACAG
           | | || |||  || | | || ||||||| | ||  ||| |   | |||  |||||||| ||  || || ||  | |||         | |||||||   ||||||||||||||||| || |||||||| |||||||| || || || |  ||||||||| ||||||||||||||||||| |||
-----------acacttaaaacctttataatgggtgagaagattga-aatct--ctaatgccatttcttgtgtagttcttttacaatttttcctttaaagcttttgttttacagGTGTATTCAAATCTTGATGGCAACAGATCTCATGTAGTAAATACCGCATGGGCTATGCTGGCTCTCATTGATGCTGGGCAG
















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|31459603|gb|CD401631.1|CD401631
EST:     AGCTTCCTTCTGGTGGCTGGGGAGAGAGCTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
EST: gi|11689289|gb|BF596965.1|BF596965
EST:     AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
EST: gi|42723073|gb|CK768972.1|CK768972
EST:     AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
EST: gi|8827016|gb|BE210746.1|BE210746
EST:     AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGACGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
EST: gi|51344264|gb|CO984997.1|CO984997
EST:     AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
EST: gi|193391350|gb|FK355031.1|FK355031
EST:     GAGAGAGTTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: GAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
EST: gi|10253317|gb|BE821083.1|BE821083
EST:     AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
EST: gi|7326817|gb|AW620615.1|AW620615
EST:     AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAG                         GTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG
genomic: AGCTTCCTTCTGGTGGCTGGGGAGAGAGTTATCTGTCCTGTCAAAACAAGgtcaaatttg ... ttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttaattgatgagatttcttgagttatttttctaacaatttgtttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGGGCTATGTTGGCTCTCATTGATGCTGGACAG
                               ttctaac  putative branch site (score: 1)
                                        tttgttttt  putative PPT
                         ttatttttctaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttgcatcaagattttaaattaacattgagtgagaatactggcaatttaattgatgagatttcttgagttatttttctaacaatttgtttttgttcagGTGTATTCAAATCTGGAAGGCAACAGGTCTCATGTGGTCAACACTGGGTGGGCTATGTTGGCTCTCATTGATGCTGGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
-ttttgca
- - - - - - - - - - - - - - tgagtga
- - - - - - - - - - - - - - - - - - -atactgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgag