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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaagtagtaaagcaactctttaatattcctgtgaatgctggtaaattaaatatatgcagtttcttatgcattttttccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

Basic information

species Glycine max
transcript GLYMA12G29120.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 3'ss of exon 10
--ttcaagtagta--aagcaactctttaatattcctgtgaatgctggtaaattaaatatatgcagtttcttatgcattttttccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
  || |||||| |  ||     |||||  || || | | || |  |  ||| |||||    |  | |  || || |  || ||   ||    ||||    |||||| |||||||| ||||| |||||| ||||||||||| |||||||  |||| || || || ||||||||||| ||||| ||||| ||  || | ||||| |
tctttaagtaggactaactttgtctttgctaatcatat-aacgacg--aaagtaaattgtagtggctatttttgaaagttgtctgtttttg-tttgttcgacagGTCTACTATGTGTATGGATTCATGTTACTGGTTTTTGTGATTCTCGTCATAGTGACGGTGTGTGTGACAATCGTGGGTACATATTTCCTGCTGAATGCAG

upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0041g00680.t01 (Vitis vinifera), 3'ss of exon 10
ttcaagtagtaaagcaactctttaatattcc-tgtgaatgctggtaaattaaatatatgcagtt-tcttatgcattttttccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
   || |       |   | ||  | || || | | |||    |   | |   | | ||   |  ||||||     |  |          | ||   ||||||| || ||||| |||||||| ||| | || |||||  |||||||||| |||||||| || ||||| ||||||||||||||||| || ||||| |||||||
--taattctctgttcttttattggagatgccatttaaatttatgctgactgtgtttgtggcttaatcttattatgctgctttgtgatttttgtgctcaacagGTATATTATGTATATGGCTTTATGTTGCTTGTTTTCATGATTCTTATGATTGTTACAGTCTGTGTAACAATTGTGGGGACATATTTCTTGTTGAATGCTG

upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0035g00280.t01 (Vitis vinifera), 3'ss of exon 10
-------ttcaagtagtaaagcaactctttaatattcctgtgaatgctggtaaattaaat-atatgcagtttcttatgcattttttccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
       |     |  |  || || ||      | |  |||   ||   | |  | ||||  | ||||||   | ||  |  ||||   ||     | ||     |||||||| |||||||||||||| |||||||||||||| |||||||| || ||||| ||||||||||||||||| ||||| |||||||| ||| |||||||||
ctctctctctctatttttgagaaattc----ggactattgtt--tgacaggagttcaaattgtttgcagtggatgataaacattttttgctgt--ttgtgctgggcagGTGTATTATGTCTATGGCTTTATGCTACTGGTTTTCCTGATTCTCATAATTGTCACTGTTTGTGTGACAATAGTGGGAACATACTTCTTGCTAAATGCTG

upper sequence: GLYMA12G29120.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ15096 (Selaginella moellendorffii), 3'ss of exon 11
ttcaagtagtaaagcaactctttaatattcctgtgaatgctggtaaattaaatatatgcagtttcttatgcattttt-tccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
                                          ||||            |||||| ||  |  |  |  ||    |||    ||     ||||| ||||| |||||||| |||||||| || || ||| |||| ||  ||||||| || ||||||||||| || ||||| || |||||  || ||||||| |
------------------------------------------gtaacccggtcgagcccagttttttcagtctgctgatctgagtccgtggtgcatggcagGTCTACTACGTCTATGGTTTCATGCTGCTCGTGTTTGTGATCCTCCTCATTGTCACGGTTTGTGTGACCATCGTGGGCACGTACTTCCTGCTAAATGCGG

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|193493779|gb|FK461425.1|FK461425
EST:     ATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: ATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|37995726|gb|CF807315.1|CF807315
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|16347100|gb|BI972695.1|BI972695
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGCTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|6341551|gb|AW164375.1|AW164375
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT
EST: gi|26268557|gb|CA819620.1|CA819620
EST:     GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAG                         GTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTACCATT
genomic: GCATATTCATCGAGATGTATTTTGTATTCACTTCCTTCTGGAATTACAAGgtgaattaaa ... tgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattaaatatatgcagtttcttatgcattttttccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG
                                          ctttgac  putative branch site (score: 4)
                tttcttatgcattttt  CT-rich tract
     aatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaagtagtaaagcaactctttaatattcctgtgaatgctggtaaattaaatatatgcagtttcttatgcattttttccccttccactttgacaaacagGTGTACTATGTCTATGGCTTCATGCTACTGGTTTTTCTGATTCTTATCATTGTTACTGTTTGTGTGACAATTGTGGGGACATACTTTTTGTTAAATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - caactct
- - - - - - - - - - - - - attcctg
- - - - - - - - - - - - - - - - - gaatgct
- - - - - - - - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - tatatgc