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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctgtgtaggacgcatgttaacaaaacctgtttgttttccgtaatgttaatgattgtattctcttttcatctaaacatgttaaattcatatttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAGTTAATTAGACTGGCAGAAACAGGTATCTTCAATCTTGGCCATGCTGTTT

Basic information

species Glycine max
transcript GLYMA08G00740.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G00740.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0031g03150.t01 (Vitis vinifera), 3'ss of exon 7
---gcctgtgtaggacgcatgttaacaaaacctgtttgttttccgtaatgttaatgattgtattctcttttcatctaaacatgttaaattcatatttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAGTTAATTAGACTGGCAGAAACAGGTATCTTCAATCTTGGCCATGCTGTTT
      ||   |  |           || |  |      || | ||| || |    |||           |  | |    ||   ||  | || |   | |||||| |||| |||||||| ||||| |   |||||||||| |||||||| |||||  |||  ||||||||||| ||||||||||||||       |||||||
taatattgaagataatttgcacccgtaacaattcccatcttcctgtactggtttccatttggccactccatttttttcgtataacaatctaatgt---aacagATAAAAGTCATTGGCTCATATGGAGCACGGGCAAGGCAGGATCTTCCCAAGTTGGTTAAGCTGGCAGAAACCGGTATCTTCAATCTCAAGGCAGCTGTTT
















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|193532183|gb|FK491919.1|FK491919
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|254331227|gb|GR845806.1|GR845806
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|254332625|gb|GR843995.1|GR843995
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|209714516|gb|BW684879.1|BW684879
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|21639017|gb|BM140063.1|BM140063
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|4303037|gb|AI443419.1|AI443419
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|254330135|gb|GR839688.1|GR839688
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|6848282|gb|AW350572.1|AW350572
EST:     AAGCTGGNTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|11688889|gb|BF596565.1|BF596565
EST:     TGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: TGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|254329031|gb|GR833403.1|GR833403
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|254331228|gb|GR845807.1|GR845807
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGGCAAGGCAAGATCTTCCAAA
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCA-GGGCAAGGCAAGATCTTCCAAA
EST: gi|192330985|gb|FK023126.1|FK023126
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
EST: gi|254332624|gb|GR843994.1|GR843994
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAG                         ATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCAGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaatgattgtattctcttttcatctaaacatgttaaattcatatttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAGTTAATTAGACTGGCAGAAACAGGTATCTTCAATCTTGGCCATGCTGTTT
                        atctaaa  putative branch site (score: 3)
                           taaacatgttaaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctgtgtaggacgcatgttaacaaaacctgtttgttttccgtaatgttaatgattgtattctcttttcatctaaacatgttaaattcatatttgagcagATACAAGTTATTGGCTCCTATGGGGGCAGGGCAAGGCAAGATCTTCCAAAGTTAATTAGACTGGCAGAAACAGGTATCTTCAATCTTGGCCATGCTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT