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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaagcttttgaacctgatttactggattcttttgtagcttcattgataacattatcatttaaagtcaatgtgatctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG

Basic information

species Glycine max
transcript GLYMA02G31320.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G878139_T02 (Zea mays), 3'ss of exon 3
----------ggaagcttttgaacctgatttactggattcttttgtagcttcattgataacattatcatttaaagtcaatgtgatctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
          |  | || ||  |||   | | |||  |||| | |||| |    ||  | ||| ||  ||   | || ||    | | || ||| | ||      ||||||||||||| ||||||||||||||| | || || || ||  ||||||| || |||||||||||||||   ||| |||||
tagagcctgtgttaactatt--accctttcttctgacttctgtagtagatgttctggca-catgat--ttggcattctataaactgtttttgcttacttt-----tgcagGTCATTGGCTGGTCAATGTGGTTTGCAGAGTACCTCTTTTTGGAGAGGAGCTGGGCCAAGGATGAAAAGACACTAAAG

upper sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G57650.1 (Arabidopsis thaliana), 3'ss of exon 5
ggaagcttttgaacctgatttactggattcttttg-ta-gcttcattgataacattatcatttaaa-gtcaatgtgatctattagctaagttccaatg----tgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
       |||||     | | | ||  ||   ||  ||  ||||   |      |||||  ||| |  |  ||   |   || | |  | ||   |      | |||||||| || |||||||||||||| || || ||||| || ||||| |||| |||||||||||||||| ||||  |||||
-------tttgagaaaaaatcattgttttaggttaatacacttctccgccttttttatctgttacatattcatagtactcataaacagaattttcacacacatacagGTCATAGGCTGGTCAATGTGGTTCTCGGAGTATCTCTTTCTGGAAAGAAATTGGGCCAAGGATGAAAGCACTCTAAAG

upper sequence: GLYMA02G31320.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0007g08110.t01 (Vitis vinifera), 3'ss of exon 5
ggaagcttttgaacctgatttac-tggattctt--ttgtagct--tcattgataacattatcatttaaagtca-atgtgatctattagctaagt-tccaatgtg--cagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
         |  |  |  | | | |  ||| ||  ||| |  |  |||||||  || ||  ||  |  |   | ||      ||   | || || |||||| |   ||||| || ||||||||||||||||||||||| ||| | || ||||| ||||  ||||||||||||||| ||| | |||||
---------tagatgtcgtctgcatacatttttctttgcaattgctcattgaacactttgacacctctatatatatacaggataaatgttatgtgtccaatttattcagGTGATAGGTTGGTCAATGTGGTTTTCTGAGTATTTATTTCTGGAAAGAAACTGGGCCAAGGATGAAAGCATAATAAAG

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|19348278|gb|BM892810.1|BM892810
EST:     GCCTTGGCAGCACACTTGCTGTGATGAAGAAATCTTCAAAGTTTCTACCG                         GTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGT
genomic: GCCTTGGCAGCACACTTGCTGTGATGAAGAAATCTTCAAAGTTTCTACCGgtatgttttg ... caatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGT
EST: gi|208051669|gb|GD854746.1|GD854746
EST:     GCCTTGGCAGCACACTTGCTGTGATGAAGAAATCTTCAAAGTTTCTACCG                         GTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTG
genomic: GCCTTGGCAGCACACTTGCTGTGATGAAGAAATCTTCAAAGTTTCTACCGgtatgttttg ... caatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTG
EST: gi|13791554|gb|BG654145.1|BG654145
EST:     GCCTTGGCAGCACACTTGCTGTGATGAAGAAATCTTCAAAGTTTCTACCG                         GNCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGT
genomic: GCCTTGGCAGCACACTTGCTGTGATGAAGAAATCTTCAAAGTTTCTACCGgtatgttttg ... caatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataacattatcatttaaagtcaatgtgatctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG
 tgataac  putative branch site (score: 2)
      attatcatttaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaagcttttgaacctgatttactggattcttttgtagcttcattgataacattatcatttaaagtcaatgtgatctattagctaagttccaatgtgcagGTCATTGGTTGGTCAATGTGGTTTTCTGAATATCTTTTCCTGGAGAGAAGTTGGGCCAAGGATGAACGCACATTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - gcttttg
- - - - - - -cctgatt
- - - - - - - - - - - - - - - - - - agcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtg