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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttctatatgttttttaaatttaaattaattttttcaattatattttctaagctagccactttgatgtatcttgaaattattagaattctcaaag...

Basic information

species Glycine max
transcript GLYMA10G38590.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38590.1 (Glycine max), 5'ss of exon 16
lower sequence: GRMZM2G025854_T02 (Zea mays), 5'ss of exon 16
AATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttctatatgttttttaaatttaaattaattttttcaattatattttc-taagctagccactttgatgtatcttgaaattattagaattctcaaag-----------------------------------------------------
|||||||||| || || |||||||| || || |||||  |||| || || || |||||||| || || |||||||||||  | ||||| ||||||||||||||       |  |  || | |  | || |||   ||  |||||| | | ||  |||| |    ||   || |  | | || || |||    ||                                                            
AATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAGAGAAGGATGGCATCTGgtaagaagtaaattacttatcagctgtagattttgttaatcaattttttctttgtaagttctaaacagagaagc-tttggacatcattcatgtttctgtttgtgtgaaatgtctgtagacaacttccatactcttatcaactcttgactctcag

upper sequence: GLYMA10G38590.1 (Glycine max), 5'ss of exon 16
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 5'ss of exon 16
AATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttctatatgttttttaaatttaaattaattttttcaattatattttctaagctagccactttgatgtatcttgaaattat-tagaattctcaaag
|||||||||| ||||||||||||||||| || |||||  | || || |||||||| ||||| ||||||||||||||||| |||||||| ||||| || |||||   |||  ||  | |  |       ||| | |   | |   |    | |  ||  |  ||   |    | ||  |   || |   | || | |   | 
AATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTGAGAAGGATGGAATATGgtaatcttccttaaatctaatgctcactaataactggatacttatgcgatatgcaacgtttccgtctaatgggattgtatcatcacacataagtttgcga-

upper sequence: GLYMA10G38590.1 (Glycine max), 5'ss of exon 16
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 5'ss of exon 16
AATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttctatatgttttttaaatttaaattaattttttcaattatattttctaagctagccactttgatgtatcttgaaattattagaattctcaaag---
||||||||||||| |||||||||||||| || |||||  |||| |||||||| ||||||||||||||||||||||||||||||||||| |||||||| |||||  | |||| || |  |   |||   | |   ||||||    |  |  || |  |  |   |     ||  | |   |   |  |  ||  | |||     
AATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAGGATGGCATATGgtaagtctctaaatttactagtaat---agtgcctttttttgcctcaagattgtctgtaacttaaagcaattcaacccaacgatgctttaagccccaactctt

upper sequence: GLYMA10G38590.1 (Glycine max), 5'ss of exon 16
lower sequence: EFJ34621 (Selaginella moellendorffii), 5'ss of exon 15
AATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttctatatgttttttaa--atttaa--attaattttttcaattatattttctaagctagccactttgatgtatcttgaaattattagaattctcaaag
| |||||||| ||||| ||||| || || ||  ||||  ||||||| || || ||||||||||| || |||||||| |||||||| || ||||| ||||||||   ||||||   ||     |  || |||  | || ||   ||    |   ||| ||| | ||                                       
AGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTGAAAAGGATGGAATCTGgtaagcttctatcacttcgcagatgatgtaaccagtagttacatcttgcacggtttttaaaccag---------------------------------------

upper sequence: GLYMA10G38590.1 (Glycine max), 5'ss of exon 16
lower sequence: EFJ32824 (Selaginella moellendorffii), 5'ss of exon 15
AATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttctatatgttttttaaat--ttaaattaattttttcaatt---atattttctaagctagccactttgatgtatcttgaaattattagaattctcaaag
| |||||||| ||||| ||||| || || ||  ||||  ||||||| || || ||||||||||| || |||||||| |||||||| || ||||| |||||||||  |||| |   |||   ||||  |  ||  | |  || ||  |   |   ||| ||| | ||                                       
AGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTGAAAAGGATGGAATCTGgtaggcttctgt-catttcgcaaatgatgtaaccagtagttacatcttgcacggtttttaaaccag---------------------------------------

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|57574855|gb|CX547830.1|CX547830
EST:     GAGAGTTTTGGACCAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTG                         GGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAT
genomic: GAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttct ... ccaattacagGGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAA
EST: gi|22541844|gb|BU091687.1|BU091687
EST:     GAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTG                         GGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAA
genomic: GAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttct ... ccaattacagGGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAA
EST: gi|15203242|gb|BI426010.1|BI426010
EST:     GAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTG                         GGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAA
genomic: GAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttct ... ccaattacagGGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAA
EST: gi|120494261|gb|EH222428.1|EH222428
EST:     GAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTG                         GGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAA
genomic: GAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttct ... ccaattacagGGCTGTCTTAGCTTGGCTTTCTATTATTGCACATCGCAACAAAGACAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTGAGAAAGATGGCATCTGgtagatttctatatgttttttaaatttaaattaattttttcaattatattttctaagctagccactttgatgtatcttgaaattattagaattctcaaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG