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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg...

Basic information

species Glycine max
transcript GLYMA19G36450.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36450.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g15370.1 (Oryza sativa), 5'ss of exon 3
CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg
|  ||   ||  |||| || |||||| |||| |||||||||||||||||  |||| || || |||||| | || || ||  ||||||||||||| ||||||       |||| || | |     ||| ||  |  | |||| ||   |||  |  | || |  | |   |   ||  |||  ||| |||   |       
CACATGTGGAAAATGGAGACATGTGCGTTGTGCTTAATGCAAAAGATATCAGTGTTACAGGAAGAAAAATGACCGATAAAATCTACTACTGGCACACAGGg-------tttgtatgttt----ctagctaatactgttgaa-taccttttggttttatt-atttacaattgtgtcttatgtgttttttcaaatag-----

upper sequence: GLYMA19G36450.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G044584_T03 (Zea mays), 5'ss of exon 3
CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg
|  ||   ||  |||| || ||||||||||| ||||||||||| |||||  |||| || || || ||| | ||||| ||| | ||||| ||||||||||||  |||   |  ||   | |  |  ||||       |    || ||    | ||  |||   ||| ||||  ||  | || |||    |    ||     
CACATGTAGAAAATGGAGACATGTGCATTGTACTTAATGCAAAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTATTGGCATACAGGgttagtaaatccca---gcaaaagaagttgtcgatcacattatttttgagattaacttttt-cttgttatgcatttattgatttatacccaaatag----

upper sequence: GLYMA19G36450.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G163473_T02 (Zea mays), 5'ss of exon 3
CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg
|  ||   ||  |||| || ||||||||||| ||||||||| | |||||  |||| || || || ||| | ||||| ||| | ||||||||||||||||||  ||| |   |||       | || |||| |     |   | ||| |||  ||  |||   ||| ||||          ||||  | |    ||     
CACATGTGGAAAATGGAGACATGTGCATTGTACTTAATGCACAGGATATCAGTGTTACAGGAAGGAAAATGACAGATAAGATTTACTACTGGCATACAGGgttagtacccagcaaaaaatttgttggttacattatttatgagatt-tttgttaactttct-cttgttatgt--------gtttattcccaaatag----

upper sequence: GLYMA19G36450.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0171g00250.t01 (Vitis vinifera), 5'ss of exon 3
CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg----
| |||||||| ||||||||||||||||| || ||||||||||| ||||| | ||| || || || ||||||||  | ||| | ||    |||||||| ||| |||  |  |   |   |  | |||||| |      | |   |      |||  |    | || | |  |||| ||  ||  |   | |||||          
CAAATCGTGAAGATGGGGATATGTGCATCGTGCTTAATGCAAAGGATATCTCTGTCACAGGAAGGAAACTTACTAATAAGTTTTATCGTTGGCATACCGGgtaagcaccct-tgtgcttggttttagttggttttagtcatgaacag---aatgttggacaactacatgaaaataaagggggctatgtttggtttccacagcag

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|151395057|gb|EV264928.1|EV264928
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|57575446|gb|CX548421.1|CX548421
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|31458202|gb|CD400230.1|CD400230
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|192333033|gb|FK024682.1|FK024682
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|7286003|gb|AW598490.1|AW598490
EST:     TGTGTGACTGGGAGATAACTTACAGACAAGGTCTACTACTGGCATACANG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|11274196|gb|BF324564.1|BF324564
EST:     TGTGTGACTGGGAGANAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCANATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|208233303|gb|GE031926.1|GE031926
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|151406922|gb|EV276737.1|EV276737
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|6725962|gb|AW310361.1|AW310361
EST:     GAGAAAAC-TACAGACAAGGTCTTACTA-TGGCATACAGG                         GTATATTGGCAACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: GAGAAAACTTACAGACAAGGTC-TACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
EST: gi|6502133|gb|AW203506.1|AW203506
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGGCCACCTCA-GCAAAGGACTCTAAAG
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGG-CCACCTCAAGCAAAGGACTCTAAAG
EST: gi|298175327|gb|HO015986.1|HO015986
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGA
EST: gi|192300730|gb|FG991112.1|FG991112
EST:     TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGG                         GTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA
genomic: TGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctt ... tggtatgtagGTATATTGGCCACCTCAAGCAAAGGACTCTAAAGGATCAAATGGCCAAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAATCGTGATGATGGGGATATGTGCATTGTTCTTAATGCAAAAGATATTTGTGTGACTGGGAGAAAACTTACAGACAAGGTCTACTACTGGCATACAGGgcaagtgctttgcatttgtactattagttagaagggatgaaatattatttaatagttttgagcttcttataaatcaaatggttttcttctggttaaggtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA