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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaacaggatgctcatgtaatataaaacttgattttattatagttcagacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG

Basic information

species Glycine max
transcript GLYMA11G15900.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os05g03480.2 (Oryza sativa), 3'ss of exon 6
agaaacaggatgctcatgtaatataaaacttgattttattatagttcagacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG
| | |     |     |    |  | ||    |  ||||    ||| | |  | |   || |    |   |   || || | |    |     |  ||||||||| ||||| |||||||| ||| ||||||| |||||||| || || || ||||| ||||||||||| ||||| ||
aaacatctcttagcggtagcttccagaaaagcaagttatgtctgtttataggtctatagacataataagcctgctagttcactaaagttgggagtttcagGTTGTGTATGCAAAAACAGATATAGCTGCTGGATCAAAAGGAATAACCGCGTTCATAATTGAGAAGGGGATGCCCGG

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G052630_T02 (Zea mays), 3'ss of exon 5
------agaaacaggatgctcatgtaatataaaacttgattttattatagttcagacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG
         ||  | || ||| | |  |  || |  |  || | || |   ||     | ||| |  |    |     |  |||      |||||   |    |||||||| ||||| ||||||||  || |||| || |||||||| || ||||||||||| || ||||| || ||||| ||
ccactccacaatcgcatcctctt-tgttggaagagctacttgtcttgtttctc-----tttgcagccataaaaccttgccaattcatccatgttggggttttacagGTTGTTTATGCAAAAACAGATCTAGCTGCGGGATCAAAAGGAATAACTGCATTCATAATCGAGAAAGGGATGCCCGG

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G381051_T03 (Zea mays), 3'ss of exon 6
agaaacaggatgctcatgtaatataaaacttgattttattatagttcagacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG
          |  |  ||   |    |  || |||    |||  ||    ||  | |||       ||    |  |||      |||||   |    |||||||| || || ||||||||  || |||| ||||||||||| || ||||||||||| || ||||| || ||||| ||
---------gtatttttgctcttcttacattcattcccctatgctttctgcac-tcctgt-----tatcctgctaattcatccatgttgggattttacagGTTGTTTACGCAAAAACAGATCTAGCTGCAGGGTCAAAAGGAATAACTGCATTCATAATCGAGAAAGGGATGCCCGG

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G052630_T03 (Zea mays), 3'ss of exon 4
------agaaacaggatgctcatgtaatataaaacttgattttattatagttcagacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG-----------------------
         ||  | || ||| | |  |  || |  |  || | || |   ||     | ||| |  |    |     |  |||      |||||   |    |||||||| ||||| ||||||||  || |||| || |||||||| || ||||||||||| || ||||| || ||||| ||                       
ccactccacaatcgcatcctctt-tgttggaagagctacttgtcttgtttctc-----tttgcagccataaaaccttgccaattcatccatgttggggttttacagGTTGTTTATGCAAAAACAGATCTAGCTGCGGGATCAAAAGGAATAACTGCATTCATAATCGAGAAAGGGATGCCCGGGTACAGAACCACTCCATTATCTT

upper sequence: GLYMA11G15900.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 3'ss of exon 7
---agaaacaggatgctcatgtaatataaaac-ttgattttattatagttca-gacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaat-cagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG
      |  || | ||    |  ||| |  |   |||||||   ||  ||    | ||   ||     |   ||| ||     ||||  | ||||| ||  | |||||||| ||||| ||||| || || || |||   |||||||| ||||| ||||| ||||| |||||||||||||||||
tctcatataagaaagcagtagctatacactatgctgatttttccatgatttgcaaaattctcttttgtttgttagaac-----tgat-atattgaactgggttcagGTTGTTTATGCGAAAACGGATATTACAGCTCATTCAAAAGGAATTACAGCATTTATCATCGAGAAGGGAATGCCTGG

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|17400326|gb|BM177108.1|BM177108
EST:     TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTA                         GTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
genomic: TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTAgtaagtttct ... attgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
EST: gi|7030287|gb|AW460070.1|AW460070
EST:     TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTA                         GTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
genomic: TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTAgtaagtttct ... attgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
EST: gi|254338023|gb|GR849655.1|GR849655
EST:     TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTA                         GTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
genomic: TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTAgtaagtttct ... attgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
EST: gi|16346614|gb|BI972209.1|BI972209
EST:     TTAATGGGATCTATATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTA                         GTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
genomic: TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTAgtaagtttct ... attgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
EST: gi|15814693|gb|BI786968.1|BI786968
EST:     TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTA                         GTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA
genomic: TTAATGGGAACAAGATGTGGTGTACTAATGGGCCAGTTGCTCAAACATTAgtaagtttct ... attgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG
                              atttgat  putative branch site (score: 5)
                             tatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaacaggatgctcatgtaatataaaacttgattttattatagttcagacatatgctgagaatgcatagcacgtatttgattgtgttgaattgaatcagGTTGTCTATGCTAAAACAGACATAACTGCTGGGTCAAAAGGCATTACTGCATTCATCATTGAGAAGGGAATGCCTGG

- - - -ggatgct
- - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcacgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattgtg