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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

Basic information

species Glycine max
transcript GLYMA08G23760.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
---ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
     |    |    ||| |  ||||  | |     | |   || | ||  | |||           | |||   |||| | ||  | || |    ||  |||||  ||||||||||||| ||||||||||| || || || ||||||||||| || |||||||| || ||||  || ||||| ||| ||||||||||| |||
gtttgagctcatactctgtttgttactgatagata-acacggaagttatggttaatat---------tctctctcttttgcttgggcttgttggctgg--cagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA

upper sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 10
ataaaaaactgactgataattacgta-caagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctct-tgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
      || |   |  | |  | | |   | |  |  | |   |  | ||              ||  ||   | ||| |  | | |    | | | |  ||||| | ||||| || || || ||||| |||||||| || |||||| ||||||||||||||||||||||||  || ||| |  |  |||| ||||| || |
--ggggaaattgttagtgaaaatgaaattaagatacttaactgtattgatttgcacgtcggcacatggctgaatgttttacttccgtttgttgttgatttagCTTCTTTGGGTCAATCTCATTATGGACACACTTGGTGCACTTGCATTGGCTACTGAACCACCAACAGACCAACTTATGAAGCGGCCACCTGTTGGACGGA

upper sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 6
ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatc----aatgaaaaaaggtatatcttggtttttcatgttcatgct--cttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
    ||| |    || |||| |   |||| |     ||||| |  | | |    | |  |||   | | | |      | | |  ||| |  |   ||   |||||||| | |||||||| || |||||||| ||||| || || |||||  |||||||||||||||||||||| |  || |||    |  |||||||||| || |
---caaaccaagttgttaatga---acaaagtgtagttaaagtattaagcttctatttgaaagttggacaccaacaaatattagcttccttttgttttttatacagCTTCTCTGGGTTAATCTCATCATGGACACACTCGGTGCTCTTGCTTTGGCTACTGAACCACCAACAGATCAACTTATGAGGCGGCCACCAGTTGGACGGA

upper sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
         |      |   | | ||   |    | | ||  |      ||| || ||||| ||||            |||    || |||| | | |||||  | ||||| ||||||||||||||||| ||||| || |||||||| ||||| || |||||||| || |  || ||||| ||| | || |||||  |||
-------gttagtaccttgatgcttatttgaatggttgaacttttaagacaaggataaaagatata------------atg---gtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA

upper sequence: GLYMA08G23760.1 (Glycine max), 3'ss of exon 29
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 28
-----ataaaaaac-tgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
      | |||||  |  ||  | ||    |   |      |  ||| | |      ||  ||       ||  |   |||||| | |||   ||    |||||||||| | ||||||||||||||||||||||| ||||| || |||||| ||||||||||||||||||| || |  || ||| | ||||| |||||||| ||||
gcagtgtgaaaaatgttgcttttcatggtctttcaaat--aaccaaatttagggattatttaattcttcttacatcactttttc-ttttctcactt---ggtacagCTTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAA

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|4313499|gb|AI460618.1|AI460618
EST:     ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAG                         CTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT
genomic: ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAGgtacgtatat ... ttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT
EST: gi|208270495|gb|GE071309.1|GE071309
EST:     ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAG                         CTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT
genomic: ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAGgtacgtatat ... ttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT
EST: gi|18732777|gb|BM527242.1|BM527242
EST:     ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAG                         CTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT
genomic: ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAGgtacgtatat ... ttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
                                        tgctctt  CT-rich tract
     aatgaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaaaactgactgataattacgtacaagggcagattaaaatcatcatcaatgaaaaaaggtatatcttggtttttcatgttcatgctcttgggtacagCTTTTGTGGGTTAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCACCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
-taaaaaa
- - - - ctgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgctc