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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag

Basic information

species Glycine max
transcript GLYMA19G17920.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os05g41180.1 (Oryza sativa), 5'ss of exon 2
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag
| ||||| || || ||||| ||||| ||||||||||| |||||||| ||||||||||| |||||| | |||||||||| ||| |||||||| ||||||||||| | | ||  |||     |    |  ||  | ||               |   ||| |||     ||   | ||| |  ||   || ||   | ||||||| |                                    
GTAGCATAGGGACTGGTTATGATCTTTCCGTCACCACCTTCTCCCCAGATGGCCGTGTCTTCCAGGTTGAGTATGCTGGCAAGGCCGTCGACAACAGCGGgttcg-atttagtttcaccctcccctctgttttatt---------------acccttttttgggctgtt-caactttatgctgaagttctga--tgttttttgcag-----------------------------------

upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 5'ss of exon 2
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgtt-ggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag
||||||| || ||||| |||||||| ||||| ||||| ||||| || ||||| || || |||||| | ||||||||  | || || ||||| ||||||||||| |||     |  |    |||   | | |  |||||  |  |   |     |  | | |  ||| ||  | ||    || |   ||||  ||                                                
GCAGCATAGGCACAGGATACGATCTGTCCGTTACCACCTTCTCTCCGGATGGTCGCGTCTTCCAGGTTGAGTATGCCACGAAGGCTGTCGACAACAGCGGgttcggtttaactgctcccctttctttccttccttttgctaccgcttcttcctttctgtgtgcaattat-gtaatgacgttctaatatttgttaacag--------------------------------------------

upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 2
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag
||||||| || |||||||||||||| || |||||||| |||||||| ||||| ||||| |||||| |||| |||||| |||| |||||||| ||||||||||| |       |   |         |  ||  |||    || || |     |   |||||   |  || |   | || | ||| || || |   |||  ||  ||    | ||  |  |  |                  
GCAGCATAGGCACAGGTTACGATCTGTCTGTCACCACCTTCTCCCCAGATGGTCGTGTCTTCCAGGTCGAATATGCTACCAAGGCCGTCGACAACAGCGGgttagattccactgcctcccacctcctattgtgtttttgcttcaagcct---tcacttatt---tccttttctctgttctatgtaatcttattggtttggtta-atgccatggtatttgtgaacag---------------

upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G445100_T01 (Zea mays), 5'ss of exon 2
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag
||||||| || |||||||| ||||| || |||||||| ||||| ||||||||||| || |||||| ||||||||||  | || || ||||| ||||||||||| |    ||    |   |   | ||| |  |||||   |     |   | | |||    |  |   ||||| | || ||  |||     |  | |||   ||   | |                               
GCAGCATAGGCACAGGTTATGATCTGTCTGTCACCACCTTCTCTCCCGATGGCCGCGTCTTCCAGGTCGAGTATGCCACGAAGGCTGTCGACAACAGCGGgttaga---ttccactgcctcccacttccta-ttttgtttt----gcttgacttgttccccgtttt-ctatgaatcttattgatgaagccatggtattt---gtgaatag-------------------------------

upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 1
lower sequence: AT2G27020.1 (Arabidopsis thaliana), 5'ss of exon 1
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag
| ||||| ||||| || |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || || ||||| ||||| ||||| ||||| ||     ||| | || ||  ||    |   || |   |  | ||||  ||| || |  ||   ||  ||||||       | || |  |      || |  |||| ||    || |    ||     ||  | | ||
GTAGCATTGGAACTGGGTACGATCTCTCCGTCACCACTTTCTCTCCCGATGGCCGTGTTTTCCAGATCGAGTACGCCGCTAAAGCTGTCGACAACAGTGGgttagt-tggctttatcttcttcgatcttcgccctttag--tagatcggatttagcttctgaaaactttgagatttt-------ggttatcgacacgaattagggtttgttaaaagtctttccctttttttttcttcgcag

upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 5'ss of exon 1
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag
||||||| ||||| || ||||||||||| |||||||| ||||| || |||||||| |||||||||||||| || || |||||||| |||||||||||||||||  | ||   | || | ||||  ||  |  ||||  ||   |||    |   ||||  |   |||  | |  |        |||        |     ||                                       
GCAGCATAGGAACTGGATACGATCTCTCTGTCACCACATTCTCTCCTGATGGCCGCGTTTTCCAGATCGAATACGCCGCCAAAGCTGTCGATAACAGCGGgttaattctccatcttctctttttttttttttttttttaacctaaatc--atctgtttggttgctaagaaagggtgggagaaatgaacggaacctcaaaatt---------------------------------------

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|298166742|gb|HO010181.1|HO010181
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|151409523|gb|EV279331.1|EV279331
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|151406675|gb|EV276490.1|EV276490
EST:     TGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: TGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|151411404|gb|EV281215.1|EV281215
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|192334682|gb|FK025887.1|FK025887
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|151409103|gb|EV278911.1|EV278911
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GCCTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|192324735|gb|FK018771.1|FK018771
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|192325082|gb|FK017498.1|FK017498
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|8827689|gb|BE211419.1|BE211419
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|26048077|gb|CA784674.1|CA784674
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|192325978|gb|FK016655.1|FK016655
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|298176424|gb|HO026659.1|HO026659
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|254321256|gb|GR827705.1|GR827705
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|16347339|gb|BI972934.1|BI972934
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|20498037|gb|BQ272967.1|BQ272967
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|26047788|gb|CA784463.1|CA784463
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
EST: gi|6726863|gb|AW311282.1|AW311282
EST:     GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGG                         GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG
genomic: GGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactt ... tttgttgtagGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCATCGGAACAGGTTACGATCTCTCCGTCACCACTTTCTCCCCCGATGGCCGTGTTTTCCAGATCGAGTATGCTGCCAAAGCCGTCGATAACAGCGGgttggtactttttttttttttttaattcgtggttttgaaattgaaacggaaatagtttattgaataattatgatttttttttgtgattttgtatttttttttgtatttggtagtgatcctagatttgaaactttgttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC