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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgagattgagatatatggctatcttacaaaattgtcagaacagattgggaaattcttaatttgaaaaatacttaaaagttaaaaaacctcgttttgcag

Basic information

species Glycine max
transcript GLYMA17G00580.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 5'ss of exon 11
GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgagattgagatatatggctatcttacaaaattgtcagaacagattg--ggaaattcttaatttgaaaaatacttaaaagttaaaaaacctcgttttgcag
 |||||||| || || |||||||||||| ||||  | ||||| |||||| ||||||||||||| || ||||||||||||||| | ||||| || ||||| || ||     |   |    ||   |||     || |  |  | | ||   |   || ||| |||  || |   | |     |  | |               
TGAGAGATACATGGTAACATATAACCCCGCAAAGGATAAGGTATATGCTTTGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCCATgtaagcacctgtcctc--actgcattaagggttttttggccccgtttattgtttatcctttattctaacatggcgttctgctgtacag--------------

upper sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 11
GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgag-attgagatatatggctatcttacaaaattgtcagaac-agattgggaaattcttaatttgaaaaatacttaaaagttaaaaaacctcgttttgcag
 ||||| || ||||| |||||||||||  ||||  ||||||| |||||| |||||||||| || || ||| ||||||| ||||| ||||| || ||||| || || ||||| | | | || ||    ||||  ||| ||   | | | |||  || | |   |     | ||  |   ||   ||      | | ||| |||
TGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCCATgtaagtattgata-acaaggtta----acaactttggcaatgccatactggtcaaatttgtttgcattatatcatcctaatcaaatgtgttttggtttacag

upper sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 11
GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgagattgagatatatggctatcttacaaaattgtcagaacagattgggaaattcttaatttgaaaaatacttaaaagttaaaaaacctcgttttgcag
 ||||| |||||||| |||||||||||  ||||  ||||||| |||||| |||||||||| || || ||| ||||||||||||| ||||| || || || || ||  |    | |||  |||| |   |  |||      || | |   |   |||    |||   |  | ||    |   |       |   ||  |||
TGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTCATgtaagcgttgattgtatt-ctatttggtaggattcc----actgctaaagttcttcgcgttttctta--tcctcgtcaaccatgt--tttttattaacag

upper sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 8
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 11
GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgagattgagatatatg-gctatcttacaaaattgtcagaacagattgggaaattcttaatttgaaaaatacttaaaagttaaaaaacctcgttttgcag
 || ||||| || || || || | |||  | ||    || || |||||  |||||||  ||||||| || |||||||||||||| ||||||||||| || ||  |||     | |||  | |   |||| |   |||    ||  | |       | ||    | ||   |        |||| |  | |   | |  |||
AGAAAGATACATGGTAACGTACAGCCCTACCAAGGGTAAAGTCTATGCACTGCTCAAACATCAGGCTAACTCAGATGACATTCTCAAAGCAGCATTTCATgtaggatgattttgtatctgtttaattactattctgttgagacgaagtaa-----ttttggcctaaattttctcattcggttacatgatcatatatcacag

upper sequence: GLYMA17G00580.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 5'ss of exon 11
GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgag--attgagatatatggctatcttacaaaattgtcagaacagattg-ggaaattcttaa------tttgaaaaatacttaaaagttaaaaaacctcg--ttttgcag---
 ||||||||| | ||||||||||| || || ||    || || |||||  | || ||||||||||| ||||| ||||||||||| ||||| || ||||| |||||  |||   | ||||   | | ||      ||  |   ||| |||   |  ||   |||      ||    | ||| |   || | | |     |    || ||||    
AGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCGTTACTGAAGGATCAGGCAAAGTCTGATGACATTCTAAAAGCTGCTTTCCATgtgagcaatttgtagatatacatttttttttttgtttcctatacatattacagtgatgagtaaaaaattttcttcacatattgggaattaagatggatttaacttctgcaacag

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|14126070|gb|BG790508.1|BG790508
EST:     TGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCAC                         GCTCATGTGCTATTATTCAATTTGATAAAATCATGGAATGAAAGTAATGCC
genomic: TGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgagattga ... cgttttgcagGCTCATGTGCTATTATTCAATTTGATAAAATCATGGAATGAAAGTAATGCC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGAGATATATTGTGACATATAACCCCTCAAAACACAAGGTTTATGCTGTGCTCAAGGATCAGGCGAAGTCAGATGACATTCTGAAAGCAGCATTCCACgtgagattgagatatatggctatcttacaaaattgtcagaacagattgggaaattcttaatttgaaaaatacttaaaagttaaaaaacctcgttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG