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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaactaagactgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

Basic information

species Glycine max
transcript GLYMA07G00630.2
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 3'ss of exon 10
--aaaaactaagactgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatattttggtttttgatgttcatgctct-tgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
    ||| |   | ||| | | |  |   | | ||  ||||    ||        |         ||   |   | ||| |  | | |    | | | |  ||||| | |||||||| || || ||||| |||||||| || |||||| ||||||||||||| ||||||||||  || ||| |  |  |||| ||||| || |
ggggaaattgttagtgaaaatgaaatt--aagatac-ttaactgtattgatttgcacgtcggcacatggctgaatgttttacttccgtttgttgttgatttagCTTCTTTGGGTCAATCTCATTATGGACACACTTGGTGCACTTGCATTGGCTACTGAACCACCAACAGACCAACTTATGAAGCGGCCACCTGTTGGACGGA

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 27
aaaaactaagactgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatat-tttggtttttgatgttcatgctcttgggt--acagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
         |  |||  | | | |||   | | | |    |     | ||  |||   | |||  || ||   | | |  || |   |||  | ||    |||||  ||||||| ||||| ||||||||||| || || || ||||||||||| || ||||| || || ||||  || ||||| ||| ||||||||||| |||
---------gtttga--gct-catactctgtttgttactgatagataacacggaagttatggttaatattctctctcttttgcttgggcttgttggctggcagCTACTGTGGGTTAACCTAATCATGGATACTCTGGGTGCTCTTGCACTGGCGACAGAACCACCTACTGACCATCTTATGCAGAGACCACCAGTTGGCAGAA

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
lower sequence: GRMZM5G893864_T01 (Zea mays), 3'ss of exon 6
aaaaactaag--actgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
  |||| |||    | ||    |        | || | ||  ||  |  |   |||||    |  |        | || | |     |  | ||   |||||||| | ||||| || || |||||||| ||||| || || |||||  ||||||||||||| |||||||| |  || |||    |  |||||||||| || |
-caaaccaagttgttaatgaacaaa-gtgtagttaaagtattaagcttctatttgaaagttggacaccaacaaatattagcttccttttgttttttatacagCTTCTCTGGGTTAATCTCATCATGGACACACTCGGTGCTCTTGCTTTGGCTACTGAACCACCAACAGATCAACTTATGAGGCGGCCACCAGTTGGACGGA

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 3'ss of exon 26
aaaaactaagac--tgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
      ||  ||  ||||  |||  |  | || |  | |   || |      | | | ||||| ||||            |||    || |||| | | |||||  | ||||||||||||||||||||||| ||||| || |||||||| ||||| || || ||||| || |  || ||||| ||| | || |||||  |||
----gttagtaccttgatgcttatttgaatggttgaacttttaagac-----aaggataaaagatata------------atg---gtgttctttgatgcagCTGCTTTGGGTCAACCTTATCATGGATACTCTTGGAGCACTTGCACTAGCTACAGAGCCACCAACCGATCATCTTATGCATAGAACCCCTGTTGGAAGAA

upper sequence: GLYMA07G00630.2 (Glycine max), 3'ss of exon 26
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 3'ss of exon 28
aaaaactaagactgatagttacgtacaagggtagattaaa-aacatcatcaatgaaaaaa--aggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
    | |  ||   || ||| | |   | |||   | ||| |||   ||  | | |  |   |  | |  ||   |   |  |  |  |     | |||||||||| | ||||| ||||||||||||||||| ||||| || |||||| ||||||||||||| ||||| || |  || ||| | ||||| |||||||| ||||
--gcagtgtgaaaaat-gttgcttttcatggtctttcaaataaccaaatttagggattatttaattcttcttacatcactttttcttttctcacttggtacagCTTCTATGGGTTAACCTTATCATGGATACTCTTGGAGCACTTGCATTGGCTACTGAACCACCAACTGATCATCTTATGGAAAGATCTCCAGTTGGTCGAA

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|33390180|gb|CA853387.1|CA853387
EST:     ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAG                         CTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT
genomic: ATGTTGTGGCAGCAATAACTTCTGGTGATGTTCCTTTAAATGCAGTGCAGgtacgtatct ... ttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcaatgaaaaaaaggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA
                            ttttgat  putative branch site (score: 4)
                                        tgctctt  putative PPT
        aaaaaaaggtatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaactaagactgatagttacgtacaagggtagattaaaaacatcatcaatgaaaaaaaggtatattttggtttttgatgttcatgctcttgggtacagCTTTTGTGGGTCAACCTTATCATGGATACACTTGGGGCGCTTGCACTGGCTACTGAACCGCCAACAGACCGCCTAATGCACAGATCACCAGTTGGCCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - -ctgatag
- - - - - - - - - - - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgctc