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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgataccttagttgtttcattgaatatgtgcatactcaatgctagttctgctctgcctatttatttgactttttaatctggacttttgtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA

Basic information

species Glycine max
transcript GLYMA20G30940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30940.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g40710.1 (Oryza sativa), 3'ss of exon 1
atatgataccttagttgttt---cattgaatatgtgcatactcaatgctagttctgctctgcctatttatttgactttttaatctggac-ttttgtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA
  || | | |   ||    |   | | |  |  |||  |  |  |     | |  | | ||| | |||| |  | |  | | ||||  | |     |    |||||||||||||||||| ||||| || ||  ||||||||||||| ||||| || || ||||||||| | ||||| ||||||||||| || ||||||||||| 
-aataaaagcagggtgacctagacttaggttcggtgttttgttga-atagggtaagatttgcttgtttact--aatggtgattctgatcatcaaaatctcgcagATGGGCTATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACCGGCTCGGATTTTGTTCAACAAGTGAAGATCCTTCTCTCCAATTTTGGGATT

upper sequence: GLYMA20G30940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G019807_T01 (Zea mays), 3'ss of exon 1
--atatgataccttagttgtttcattgaatatgtgcatactcaatgctagttctgctctgcctatttatttg-actttttaatctggacttttgtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA
  | |||  |  |  || |    |  || |     | |  |  |   ||  |     | || | | | | ||  ||  || | || |       | |   ||| ||||| |||||||| ||||| || ||  |||||||||||||||||||||| || ||||||||| | ||| | ||||||||||| || |||||||| || 
aaaaatgcaagataggtagacgtaaggattcaccacgttgttgag--tacgttaagacagcttgtctctatgcgctaattcaccttgctacacatcttg-cagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTATGCAACAGGCTCGGATTTTGTTCAGCAAATGAAGATCCTTCTCTCCAATTTTGGAATT

upper sequence: GLYMA20G30940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G143469_T01 (Zea mays), 3'ss of exon 1
---atatgataccttagtt----gtttcattgaatatgtgcatactcaatgctagttctgctctgcctatttatttgactttttaatctggacttttgtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA
   | | |||   |   |     | ||||     |   ||  ||    | |  || ||  ||||      | |||   |   ||  |    || ||        ||| ||||| |||||||| ||||| || ||  ||||||||||||| |||||||| || ||||||||| | ||| | ||||||||||| || ||||| || || 
aatacacgatgggtagatgcaaagattcaccacgttcttgagtaggttaaggaagctcatctctatgcgctaattcatcagctttctacaaacctt-------gcagGTGGGCCATGTTTGGGTTTGCAGTAGGGATGCTAACAGAGTACGCAACAGGCTCTGATTTTGTTCAGCAATTGAAGATCCTTCTTTCCAATTTCGGAATT

upper sequence: GLYMA20G30940.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G34000.1 (Arabidopsis thaliana), 3'ss of exon 1
--atatgataccttagttgtttcattgaatatgtgcatactcaatgctagt---tctgctctgcctatttatttgactttttaatctggacttttgtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA
    ||| | | | |  |       |  |||     |   |  |  || ||   |  |  |||||||   |   ||    |   | ||   ||||||||    || ||||||||||||||||| || |||||  |||| |||||||||||||||||||||||  ||||||||||||| ||||||||||| |||||||| || || 
attgatgtttcttcaaattcagacatatatagcctaaagtttcacacttgtcagttggtactgcctagacaagagataactctgtgtg---ttttgttt--gtagGTGGGCTATGTTTGGTTTCGCAGTTGGTATGCTCACAGAGTATGCAACAGGATCAGACCTTGTTGATCAAGTTAAGATCCTTCTCTCAAATTTCGGCATT

upper sequence: GLYMA20G30940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0072g00120.t01 (Vitis vinifera), 3'ss of exon 1
atatgataccttagttgtttcattgaatatgtgcatactcaatgctagttctgctctgcctatttatttgactttttaa-tctggacttttgt------ttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA
      | | |||      | |||   |  |   ||| | ||||    |  |  || ||| || ||  |   |  ||   ||||    | | |      || | ||||||||| ||||| ||||||||||||||  ||||||||||||| |||||||| || || |||||||||||||||||||||||||| || ||||||||||||
------tcctttataaacattattatgttggcctata-ttaatgtatttcttcatcagccaatctagcttcttacttgggtctgtctctgtctgggatgttaatcagATGGGCAATGTTCGGTTTTGCTGTTGGGATGCTAACAGAGTACGCAACAGGCTCTGACTTTGTTGATCAAGTAAAGATCCTTCTCTCCAATTTTGGGATA

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|22525373|gb|BU084184.1|BU084184
EST:     CAGGGTCCTTTCTTTGGCTTCATTGGCAAAAATGAGATTAGCAACGGAAG                         ATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGG
genomic: CAGGGTCCTTTCTTTGGCTTCATTGGCAAAAATGAGATTAGCAACGGAAGgtaaaaaaat ... gtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGG
EST: gi|19348188|gb|BM892720.1|BM892720
EST:     CAGGGTCCTTTCTTTGGCTTCATTGGCAAAAATGAGATTAGCAACGGAAG                         ATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGG
genomic: CAGGGTCCTTTCTTTGGCTTCATTGGCAAAAATGAGATTAGCAACGGAAGgtaaaaaaat ... gtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttctgctctgcctatttatttgactttttaatctggacttttgtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA
                            ttttaat  putative branch site (score: 3)
                                        cttttgtttc  putative PPT
               tatttatttgactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgataccttagttgtttcattgaatatgtgcatactcaatgctagttctgctctgcctatttatttgactttttaatctggacttttgtttcaacagATGGGCTATGTTTGGTTTTGCTGTTGGATTGCTAACAGAGTATGCAACAGGATCAGATTTTGTTGATCAAGTAAAGATCCTTCTATCAAATTTTGGGATA

- -tgatacc
- - - - - - - - - - - - - - - - gcatact
- - - - - - - - - - - - - - - - - - - -caatgct