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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAATCAGGAGTTTACAAACACATCACAGGTTATGAACTAGGTGGTCATGCAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgatatgttcctgattgacatttcagtcccctgggacataccatctgaaatttagaattttatactgattgggtgcttttcattttttcag

Basic information

species Glycine max
transcript GLYMA19G41120.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41120.1 (Glycine max), 5'ss of exon 9
lower sequence: AT1G02300.1 (Arabidopsis thaliana), 5'ss of exon 8
CAAATCAGGAGTTTACAAACACATCACAGGTTATGAACTAGGTGGTCATGCAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgatatgttcctgattgacatttcagtcccctgggacataccatctgaaatttagaattttatactgattgggtgcttttcattttttcag
|||||||||||| ||||| |||| || ||| | | | || ||||||||||| ||||| ||||| |||||||| |||| || || || |||||||||||||| || || |||| ||| || | | | || | |||| || | | |
CAAATCAGGAGTATACAAGTACATAACGGGTACTAAGATTGGAGGTCATGCAGTTAAGCTCATTGGCTGGGGAACTTCTGATGACGGCGAAGATTATTGGgtatga----attctctggattttgattcagatcaagctgaaaaagtaat--aacattttcttgttcgttgttgcag--------------------

upper sequence: GLYMA19G41120.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 5'ss of exon 8
CAAATCAGGAGTTTACAAACACATCACAGGTTATGAACTAGGTGGTCATGCAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgatat--gttcctgattg--acatttcagtcccctgggacataccatc-tgaaatttagaat--tttatactgattgggtgctttt----cattttttcag--------------------
| ||||||||||||| | ||| |||||| ||| | || |||||||| || ||||| || || |||||||| || || |||||||||||||||||||||| | ||| |||||| || | ||| | || | | || | | ||||| || |||||| | | | | | | ||| |
TGAGTCAGGAGTTTACAGATACACCACAGGCGATGTCATGGGAGGTCATGCCGTTAAGCTGATAGGTTGGGGAACCACCGATGATGGGGAGGATTATTGGgtatctctctatctgttcctatttatcatattctataaccatagattttattttggttctatttatcatcttttataaccgtagattttgtctaagataatttcttgattatgtattctttgttgcag
















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|120493020|gb|EH221187.1|EH221187
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|9258700|gb|BE346847.1|BE346847
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCTAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|7692402|gb|AW760509.1|AW760509
EST:     GGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: GGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|21675978|gb|BQ628329.1|BQ628329
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|7925196|gb|AW831222.1|AW831222
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGTGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|192322841|gb|FK014772.1|FK014772
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|254320265|gb|GR831073.1|GR831073
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|18848714|gb|BM567826.1|BM567826
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGG
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGG
EST: gi|192312976|gb|FK003642.1|FK003642
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|6914718|gb|AW396248.1|AW396248
EST:     CAGTAAAGCTTATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|10252856|gb|BE820622.1|BE820622
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|192312975|gb|FK003641.1|FK003641
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|16282781|gb|BI945202.1|BI945202
EST:     AGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGAATAATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: AGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGG-ATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|254320264|gb|GR831072.1|GR831072
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|31476328|gb|CD418356.1|CD418356
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|209724788|gb|BW672571.1|BW672571
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|19346981|gb|BM891861.1|BM891861
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|14259461|gb|BG882369.1|BG882369
EST:     CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgat ... attttttcagCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAATCAGGAGTTTACAAACACATCACAGGTTATGAACTAGGTGGTCATGCAGTAAAGCTAATTGGATGGGGAACAACTGAAGATGGGGAGGATTATTGGgtatgttgatatgttcctgattgacatttcagtcccctgggacataccatctgaaatttagaattttatactgattgggtgcttttcattttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT