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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgatgttgttgtatttttgttagtgtgtgtttagtagcaccgtgggtctttgtcaagagctgattgcattacttgacacacggaatcttctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAAGGGGAGGTGGAGTTTCAAGTGTGTACACTTGGGAAAAATGTGACTATTA

Basic information

species Glycine max
transcript GLYMA08G47890.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 3'ss of exon 7
gtaattgatgttgttgtatttttgttagtgtgtgtttagtagcaccgtgggtctttgtcaagagctgattgcattacttgacacacggaatcttctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAAGGGGAGGTGGAGTTTCAAGTGTGTACACTTGGGAAAAATGTGACTATTA
               |||  |||  || |   | || |  |||  | ||  | | | |  |  |||| ||   | |   | |||      |||   || ||||||||||   ||||  ||||||||| |||||||  | ||| | || || ||||||||||| || ||| | |||||||||||||||||| |||| || || |
---------------gtaagtttcata-tccatattgaccagctacatgcctatat-tgtattgctgttttgttaatcagccacctactttctctgcttgcagGCAATGAGCGAGACTGAAGCTTTGAATATGAAATCAGCTTTAGAATCCAAAGGGGAGGTTGAATTTAAGGTGTGTACACTTGGGAAAGATGTCACCATAA

upper sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 7
----gtaattgatgttgttgtatt--tttgttagtgtgtgtttagtagcaccgtgggtctttgtcaagagctga--ttgcattactt-gacacacggaatcttctctcg--cagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAAGGGGAGGTGGAGTTTCAAGTGTGTACACTTGGGAAAAATGTGACTATTA
      ||| |||  | || | ||      |||||     | | || | |       |   | |      | |   || ||| ||||  |   |  |   |  |  |     ||||||||| ||| |||||||||||||| ||||||||  || ||||||| ||||| ||||  |||||  | || || |||||||| |||||||| |||||||
gtaaaaaatggatagttttttcttggccctttagtacacttcttgtggtagaagttattcatatggcttcccgggctttcatcacttcaatttattgttccccccttttgttagGCAATGGATGAAAAAGAAGCTTTGGAAATGAAGGCCACTTTGGAGTCCAAAGGAGAGGCAGAGTTCAATGTCTGCACACTTGGAAAAAATGTAACTATTA
















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|193518493|gb|FK472690.1|FK472690
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTG
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTG
EST: gi|193314660|gb|FK280894.1|FK280894
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCGAAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTC-AAA
EST: gi|6916252|gb|AW397782.1|AW397782
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
EST: gi|207843229|gb|GD816831.1|GD816831
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAAGTACAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGG-AGT-CAA
EST: gi|208119562|gb|GD917411.1|GD917411
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
EST: gi|7285216|gb|AW597703.1|AW597703
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
EST: gi|207703938|gb|GD685928.1|GD685928
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
EST: gi|192297232|gb|FG992371.1|FG992371
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAACGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
EST: gi|208079475|gb|GD877651.1|GD877651
EST:     TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAG                         GCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA
genomic: TGGGTCTGGCATTCAAGGGGAACCAGAGGATGGTGGTTGAAGCACTTGAGgtaattgatg ... tctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggtctttgtcaagagctgattgcattacttgacacacggaatcttctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAAGGGGAGGTGGAGTTTCAAGTGTGTACACTTGGGAAAAATGTGACTATTA
                           acttgac  putative branch site (score: 4)
                                          tcttctctcgc  putative PPT
                        attactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgatgttgttgtatttttgttagtgtgtgtttagtagcaccgtgggtctttgtcaagagctgattgcattacttgacacacggaatcttctctcgcagGCAATGGCTGAGAAAGAAGCTTTGGATATGAAGGCTGCTCTGGAGTCAAAAGGGGAGGTGGAGTTTCAAGTGTGTACACTTGGGAAAAATGTGACTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG