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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaaataaaacaagcaatttctttttgtggttttgtttttggtgctatctgcaaactgtgcttatgcatgattcccatttatttttcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGAAGCCT

Basic information

species Glycine max
transcript GLYMA02G40310.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G40310.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtatgcaaaataaaacaagcaatttctttttgtggttttgtttttggtgct-------atctgcaaactgtgcttatgcatgattccc--------attta---tttttcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGAAGCCT
                      |  ||    | |||   |    ||  ||||| || ||  ||||||  |  |       || || ||| ||     |  ||| | |           | |||   || ||||| |||||||||||| |||||||| | | | ||  ||||| ||||||||||||||||||| |||
gtatgtatggttaactgtgattggctgtttgacaaagttatttcttagtttttatgattcggttttttttttttccaagtatttgtaaaatgctagcacacattactttttattggggacttacctttcttcacctgcagTTTCTGAAGGGGTTGAAAATACCTTCTCTGGTATGAAAAAGAAGAAGAAGAAACCT
















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|193312586|gb|FK275222.1|FK275222
EST:     CTGAGAAGACAGAAAACCTACTCAG                         TTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTG-AAAAGAAGAAGAAG
genomic: CTGAGAAGACAGAAAACCT-CTCAGgtatgcaaaa ... tcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAG
EST: gi|151412916|gb|EV282728.1|EV282728
EST:     TGCTGATGACCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAG                         TTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
genomic: TGCTGATGACCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAGgtatgcaaaa ... tcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
EST: gi|208281966|gb|GE080176.1|GE080176
EST:     TGCTGATGACCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAG                         TTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
genomic: TGCTGATGACCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAGgtatgcaaaa ... tcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
EST: gi|208057088|gb|GD854179.1|GD854179
EST:     CCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAG                         TTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
genomic: CCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAGgtatgcaaaa ... tcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
EST: gi|58020605|gb|CX707347.1|CX707347
EST:     GGCTGAGAAGACAGAAAACCTCTCAG                         TTTCTGAGGGGGTTGAGACTGCATTTGCTGG-TTGAAAAAGAAGAAGAAGA
genomic: GGCTGAGAAGACAGAAAACCTCTCAGgtatgcaaaa ... tcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
EST: gi|16347705|gb|BI973300.1|BI973300
EST:     GATGACCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAG                         TTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA
genomic: GATGACCCTGTGGAGAAATTGGCTGAGAAGACAGAAAACCTCTCAGgtatgcaaaa ... tcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgctatctgcaaactgtgcttatgcatgattcccatttatttttcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGAAGCCT
                               ttcccatttatttttc  CT-rich tract
                                    atttatttttcactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaaataaaacaagcaatttctttttgtggttttgtttttggtgctatctgcaaactgtgcttatgcatgattcccatttatttttcacttgcagTTTCTGAGGGGGTTGAGACTGCATTTGCTGGTTTGAAAAAGAAGAAGAAGAAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC