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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGTAATCTTGTCCCTAGCAAAAGTGGTGAGGGCATTGACATGCTTGGAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttccctctgtcctttcccagcaaacctatgctttgtctttataacttgttttaaaggatgtggctccttcaaagcgaggaagtgcactcacaat...

Basic information

species Glycine max
transcript GLYMA10G10180.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G10180.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os10g33275.2 (Oryza sativa), 5'ss of exon 15
TGGTGGTAATCTTGTCCCTAGCAAAAGTGGTGAGGGCATTGACATGCTTGGAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttccctctgtcctttcccagcaaacctatgctttgtctttataacttgttttaaaggatgtggctcc--ttcaaagcgaggaagtgcactcacaat--
|||||||  |||       ||||||| ||| || |||||||| |||||||| || || ||||||||||||||  |||   || |||| ||||| ||   ||||    || ||   | |  | | ||  ||| | |      |    | ||   | ||| |   ||     | |  ||| |    | |   |    |   ||   
TGGTGGTTCTCTCAGTGAGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGGTATCTTCATTTCTCTGCACCAAGGCGTATCATAGAGTTGATCCAGgta----tctctaacttccctacaagataacttgtttgaactaaagaaaaaaggatttcagttattctatttcgtttctattttaaggtttatttttcgaacag

upper sequence: GLYMA10G10180.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G399212_T01 (Zea mays), 5'ss of exon 17
TGGTGGTAATCTTGTCCCTAGCAAAAGTGGTGAGGGCATTGACATGCTTGGAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttccctctgtcctttcccagcaaacctatgctttgtctttataacttgttttaaaggatgtggctccttcaaagcgaggaagt-gcactcacaat-
|||||||   |||   || ||||||| ||| || |||||||| |||||||| ||||| ||||||||||| ||| ||||  ||  ||| ||||| ||   ||||       |||    |      |      ||   |||||     | |   | | || ||   | ||  |  ||       |  |||| |   |   |   
TGGTGGTTCGCTTAGTCCGAGCAAAACTGGAGAAGGCATTGAGATGCTTGGGGGTTATCTTCATTTCTCGGCTCCAAAGCGTACCATAGAGTTGATTCAGgtataaccagctccactccaatatattg--tctcaactttgaaaaaaaataatatcttcaattgtttgtgttatttttgctaaaaaagttgtttttgtacct

upper sequence: GLYMA10G10180.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 5'ss of exon 15
TGGTGGTAATCTTGTCCCTAGCAAAAGTGGTGAGGGCATTGACATGCTTGGAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttccct------ctgtcctttcccagcaaacc-tatgctttgtctttataacttgttttaaag-----------gatgtggctccttcaaagcgaggaagtgcactcacaat------------------------------------------
||| || |||||  | || ||| |||  |||||||| ||||| |||||||| |||||||||||||||||||||||||| |||||  | ||||| ||| |||||||| ||| |       | || ||||  |||   |  | ||     |  ||    ||||||||               | | |   || ||    ||    |  |  |   |  |                                           
TGGCGGCAATCTCATTCCAAGCGAAACCGGTGAGGGAATTGAAATGCTTGGGGGTTACCTTCATTTCTCTGCTTCAAAGAGTGTATTAGAGTTGATACGGgtaatgctccttgagagtttctcttttcatagctttctatgtgtcaaataatttgtgcttgttttctctctctctctcttggtttaattcatttttggcatatatatagatatatgaatgtattgaaccaggcttgattttgggtgatggtgctttgcag

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|22930693|gb|BU547832.1|BU547832
EST:     GAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGG                         AAATTGCGTGGGGAGCTTGACAAGCTTCTGAACAGAAAAATTGAAGAACCA
genomic: GAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttcc ... ggacatgcagAAATTGCGTGGGGAGCTTGACAAGCTTCTGAACAGAAAAATTGAAGAACCA
EST: gi|214009875|gb|DB987523.1|DB987523
EST:     GAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGG                         AAATTGCGTGGGGAGCTTGACAAGCTTCTGAACAGAAAAATTGAAGAACCA
genomic: GAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttcc ... ggacatgcagAAATTGCGTGGGGAGCTTGACAAGCTTCTGAACAGAAAAATTGAAGAACCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGTAATCTTGTCCCTAGCAAAAGTGGTGAGGGCATTGACATGCTTGGAGGTTACCTTCATTTCTCTGCTTCAAAAAGTGTCATTGAGTTAATAAGGgtaatgttccctctgtcctttcccagcaaacctatgctttgtctttataacttgttttaaaggatgtggctccttcaaagcgaggaagtgcactcacaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttc