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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttcttgctagaataatttggtccatagagttctttctgtgattcctcatgccatgtgtactgactattaacctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT

Basic information

species Glycine max
transcript GLYMA08G24120.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24120.4 (Glycine max), 3'ss of exon 9
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
gtagttcttgcta-gaataatttggtccata---gagttctttctgtgattcctcatgccatgtgtactgactattaacctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
   ||    |  | || |  || |    ||      ||| | ||| ||| |  ||| ||  | | ||   |||  |    | || ||||| ||||||||||| ||||| |||||||| |||||||| || || || || || ||||| || || ||||||||||||||||| |||||||| |||||||
---gtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagct-tctataa-aacttatcgtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT

upper sequence: GLYMA08G24120.4 (Glycine max), 3'ss of exon 9
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 10
gtagttcttgctagaataatttggtccatagagttctttctgtgattcctcatgccatgtgtactgactattaacctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
   ||      |   || ||| ||     |  | ||||    |   || | || | ||||  |   | ||      |  | ||||| || |||||||| ||||| |||||| | |||||||| || || ||||| || ||||| || || ||||||||||| ||||| |||||||| |||||||
---gtaagatgtcacatgatt-ggcttgaaaggctcttatgttccatctttattctatgtagaaataataaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT

upper sequence: GLYMA08G24120.4 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 10
gtagttcttgctagaataatttggtccatagagttctttctgt------gattcctcatgccatgtgt---actgactattaac--ctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
||||   ||     | | | ||  || |||  |||   |   |      ||    |  |||  ||| |   |||   ||  ||   || || |||||||||||||| || ||||| |||||| | |||||||| || || ||||| || |||||||||||||| || || || ||||| || || || || ||||
gtagccattctacaactgaatttttcaataatgttggctgaatcaaaaggaactttagtgctttgtttttaacttgatacaaaatgctcttacagCCTGAAAGTGTTCGGGAGATCACTGATCTTCTTGATGCAGTTGGGAACACCACAAAAGCTACCACCAAGGGATTCGCCATTGGATCCGCGGCACTCGCAT

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|58022630|gb|CX709371.1|CX709371
EST:     GGCCCAATAGCTGATAATGCT-GAGGGAATTGTAGAGATGAGTCAGCAG                         CCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACA
genomic: GGCCCAATAGCTGATAATGCTGGA-GGAATTGTAGAGATGAGTCAGCAGgtagttcttg ... cctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACA
EST: gi|58022340|gb|CX709081.1|CX709081
EST:     TGGCCCAATAGCTGAT-ATNGCTGGAGGAATTGTAGAGATGAGTCAGCAG                         CNTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACA
genomic: TGGCCCAATAGCTGATAAT-GCTGGAGGAATTGTAGAGATGAGTCAGCAGgtagttcttg ... cctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttctttctgtgattcctcatgccatgtgtactgactattaacctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT
                                       tattaac  putative branch site (score: 1)
                                             cctttttc  CT-rich tract
                                     actattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttcttgctagaataatttggtccatagagttctttctgtgattcctcatgccatgtgtactgactattaacctttttcagCCTGAAAGTGTCCGAGAGATAACTGATGTCCTTGATGCCGTAGGAAACACAACCAAAGCTACCACCAAAGGGTTTGCTATTGGTTCTGCTGCTCTTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT