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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTAAACAATTGTGATGATGTGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatatttaggtttaagtgatgttgtgtggcgcacctattccctgtattttcaccttgctctgttgatttctttaatactgatatggaacaatctgttacag

Basic information

species Glycine max
transcript GLYMA12G00790.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00790.1 (Glycine max), 5'ss of exon 10
lower sequence: AT5G51460.1 (Arabidopsis thaliana), 5'ss of exon 10
GGCTAAACAATTGTGATGATGTGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatatttaggtttaagtgatgttgtgtggcgcacctattccctgtattttcaccttgctctgttgatttctttaatactgatatggaacaatctgttacag
| |||||||| ||||| ||||| ||||| || ||| |||| |||||||  || ||||||||||||||||||||  | ||    |  |     ||   |    |    |  |      || |||   |||    ||    |    | |                           
GCCTAAACAACTGTGAGGATGTTCTTCCAATCTATGTTGGGGATGATCGAACAGACGAAGATGCATTTAAGgtt-tgttcttataaacacattgagctaaaacatttcattaagaaatagttttgacttaaagtgcaagtaatgtcag--------------------------

upper sequence: GLYMA12G00790.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S32_182V6.1 (Physcomitrella patens), 5'ss of exon 10
GGCTAAACAATTGTGATGATGTGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaa----tatttaggtttaag-tgatgttgtgtggcgcacctattccctgtattttcacc-ttgctctgttgatttctttaatactgatatggaacaatctgttacag
|| |  |  ||    ||||| |  ||||  ||||| ||||||||||| ||||||| ||||||||||| ||||||      || ||  ||  |  || |||  | |   |  | | |||  || |||   | | ||  | ||   ||   ||| |  | ||  | ||||| | ||      
GGTTTCAAGATACAAATGATCTAATTCCACTATATCTTGGAGATGATAAGACTGATGAAGATGCATTCAAGgtaggcaccatctaccttccacctggtgtcttctattgttctttttc--tgcattgagatcattcttttggcaatgcttttcactcagaagttgaaca-tatg------
















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|31465820|gb|CD407848.1|CD407848
EST:     CTGACGAAGATGCATTTAAG                         GTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
genomic: CTGACGAAGATGCATTTAAGgtaatattta ... tctgttacagGTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
EST: gi|7692805|gb|AW760904.1|AW760904
EST:     TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATGTAAG                         GTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
genomic: TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatattta ... tctgttacagGTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
EST: gi|10847912|gb|BF071647.1|BF071647
EST:     TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAG                         GTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
genomic: TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatattta ... tctgttacagGTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
EST: gi|15287889|gb|BI471780.1|BI471780
EST:     TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAG                         GTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
genomic: TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatattta ... tctgttacagGTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
EST: gi|10234926|gb|BE803814.1|BE803814
EST:     TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAG                         GTTTTGAGAGAGGGAAATAAAGGTTATGGGAT
genomic: TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatattta ... tctgttacagGTTTTGAGAGAGGGAAATAAAGGTTATGGGAT
EST: gi|22929040|gb|BU546179.1|BU546179
EST:     TGCTTCCTATATATANTGGAGATGATCAGACTGACGAAGATGCATTTAAG                         GTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA
genomic: TGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatattta ... tctgttacagGTTTTGAGAGAGGGAAATAAAGGTTATGGGATCTTGGTGTCTTCGGCACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTAAACAATTGTGATGATGTGCTTCCTATATATATTGGAGATGATCAGACTGACGAAGATGCATTTAAGgtaatatttaggtttaagtgatgttgtgtggcgcacctattccctgtattttcaccttgctctgttgatttctttaatactgatatggaacaatctgttacag

- - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG