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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

Basic information

species Glycine max
transcript GLYMA16G09020.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
      |   |||| ||  | | | ||  ||| || || |   |    || || |      | |||| ||  | |      |||||||||||||||| || || |||||||||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| || |||||||| |||||| 
------gtacgatgaaccaaaaatctac-cttgcttttctagatttctgttttggctgactgttttgattccttat----tagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 10
gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
|||   ||  |    |  || |   |  |  || ||   |||    | | | |   || |   ||   ||| |    |  ||||||||||| |||||||| || ||||| |||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| ||||||||||| |||||| 
gtagctga-agccaaaggcacaccatgcgtattttagactcaaattttgcact---gactgatttcactttgt----tgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGA

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 10
gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
|||   ||  |    |  || |   | |    | ||   |||    | | | ||   | | | ||   |||||    |  ||||||||||| ||||| || || ||||| ||||||||||||||||| ||||| ||||| ||||| || || ||||| ||||| ||||| ||||| |||||| 
gtagctga-agccaaaggcacaccatgtttagtttagactcaaattttgcactt---actggtttcactttat----tgtcagGCTGTTGGAAAAGTCCTGCCTGAGCTGAATGGAAAACTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGATTTGACATGCCGGA

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacaagatggatggacacagattttatgctttc-tattttcagtactggtatttgtgattaggtttgttttatgaaatca-cagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
||||   |   ||    |||| || |||     | ||   || | | |  |||||  |    |  || |||  |    |||  |||||||||| || || ||||| || || ||||||||||| || || ||||| |||||||| || || || ||||| ||||| ||||| || ||||| || |
gtacccaa---atttgtacag-ttatatataaacatagcatctggaatcatatttaagccatgacttttttacttgtctcaatagGCTGTTGGTAAGGTCCTTCCGGAACTCAATGGAAAACTAACAGGAATGGCCTTCCGTGTCCCAACACCAAATGTCTCTGTTGTGGATTTAACTTGTCGAC

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G79530.1 (Arabidopsis thaliana), 3'ss of exon 10
gtacaagatggatggacacag--attttatgctttctatt-ttcagtactggtatttgtgattaggttt--gttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
|||||  |   |   |||  |  ||   | || |   ||| | |   |  || | |  |   |  | |   ||||| |||      ||||||| || |||||||||||||| || ||||| ||||| || || ||||| |||||||| || ||  | ||||||||||||||||| || ||||| || |
gtacacaa-aaactcacatggttatcgcaagcatgtaattatcctaaatcgggaatcatatctgagctgtggttttttgatcaagtagGCTGTAGGTAAAGTTCTTCCAGAACTGAATGGGAAACTTACGGGAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGAC

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------gtacaagatggatggacacagattttatgctt---tctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
                                             |||     || |||||      | | | |  |     ||       | |   | || |||| | ||  | ||| |||      |||||||| || || || || |||||  | ||||| || |||||||| ||||| |||||||| || ||||||||||| |||||||| ||| ||||    || |
gtactgtgctcattatttggaccctggtggttagatgggactgctgtaagttgtgaatggagttgtctgtaaagtctgaacataggcctgatcccaattttcgtgactcgggat-tttcatg------cagGCTGTGGGCAAGGTACTGCCAGAATTGAATGGGAAGCTCACTGGTATGGCTTTCCGTGTGCCAACTCCCAATGTGTCTGTGGTAGACCTGACCGTGCGAC

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S309_84V6.1 (Physcomitrella patens), 3'ss of exon 8
------------------------------------------------gtacaagatggatggacacagattttatgctttctattttcagtactggtat--ttgtgattaggtttgttttatgaaatca--cagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
                                                 |  ||| |   ||  |    ||| | |||  |     ||||  | |||  |  | ||   |    | |||        |||  ||||| || || || || || |||||||| ||||| || ||||| || ||||| |||||||| |||||||||||||| |||||||||||  |||||   || |
gtactgtgcacgacagttgaatccttggcgagtgcactcatgaggctgctgtaagttatgtgagcg-gaattgtctgcact---gattcaacattggcctgatcgtcgctttcctcgttcgggattttcaaacagGCCGTGGGCAAGGTGCTGCCAGAGCTGAATGGGAAGCTCACCGGTATGGCTTTCCGTGTCCCGACTCCCAATGTGTCTGTGGTGGATCTGACTGTGCGTC

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ15779 (Selaginella moellendorffii), 3'ss of exon 7
gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
                                ||| |||| |       | |      | |       |||  |   || |||||||| || || |||||||||||||| ||||| || ||||| || ||||| |||||||| || ||||| || || || || || |||||||| |||||  
-------------------------------gtctcttttaatggaccatgtccaaagtcactaaatgttttcgttttctcagGCTGTCGGCAAGGTTCTTCCAGAGCTCAATGGCAAGCTCACAGGAATGGCGTTCCGTGTCCCAACTCCAAACGTCTCAGTCGTCGACTTGACGTGCCGAT

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ32914 (Selaginella moellendorffii), 3'ss of exon 9
gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
                          | |  |  | |  |      ||      || | ||    ||||||  |   || |||||||| || || |||||||||||||| ||||| || ||||| || ||||| |||||||| || ||||| || || || || || |||||||| |||||  
------------------------gcacgtctcttttaatggaccatgtccaaagtcactaaa--tgtttt-cgttttctcagGCTGTCGGCAAGGTTCTTCCAGAGCTTAATGGCAAGCTCACAGGAATGGCGTTCCGTGTCCCAACTCCAAACGTCTCAGTCGTCGACTTGACATGCCGAT

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|254346562|gb|GR856284.1|GR856284
EST:     GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG                         GCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCA
genomic: GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... gaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCA
EST: gi|254326011|gb|GR838892.1|GR838892
EST:     GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAG                         GCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCA
genomic: GAAGAGGGGCAGCTCAAAATATAATTCCAAGTTCAACTGGTGCTGCGAAGgtacaagatg ... gaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC
                                   tttgttttatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA