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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagatatggcttagctgatggactaatttaatcttaacttgaatgcctgttacctaagatatgtcttagctaatagactaatttaatctttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACTGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA

Basic information

species Glycine max
transcript GLYMA19G41120.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g24550.4 (Oryza sativa), 3'ss of exon 11
gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagatatggcttagctgatggactaatttaatcttaacttgaatgcctgttacctaagatatgtcttagctaatagactaatttaatctttaat---tgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACTGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAG-GTGA
                                             |  |   ||| ||  ||  |  | || |||   || |  ||||     ||  |   || | | | ||||| ||      |||  ||  | ||    | ||||||| ||||||||||||  ||| || |||||||||||||| || ||||| |||||   ||||||| |||| || || || ||| | || ||  |   || 
---------------------------------------------gtaagtccttggcaaatatataagttcaat---aagtgaaatgttgcataatttgtattt-tttgagctattaataatgtttggtcggtgatactggtagGATGGGTACTTCAAGATCATAAGGGGCACAAACGAATGTGGCATCGAAGAAGATGTTGTTGCTGGTATGCCCTCGACGAAGAACATGGTGAGGAACTATG-

upper sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G02305.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagatatggcttagctgatggactaatttaatcttaacttgaatgcctgttacctaagatatgtcttagctaatagactaatttaatctttaa-ttgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACTGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
                                                 |   ||          | |||  ||  || ||||     | |    || |||| |   |  | |   ||||   ||  |||||  || || |||||||| |||||||||||| | ||||| |||||||||||||| |||||| | | |||    |||||||| |||||   ||  ||| | || | ||   | |
------------------------------------------------gtaagttcttcttctctccaatcaaacttttactttcgacctt----ccaaagaaaccacagaacct-tagat--atagaatctgaaaatttcagGATGGGTACTTCAAGATCAGGAGAGGAACAAACGAATGTGGCATTGAACATGGTGTTGTAGCTGGTTTACCTTCAGACAGGAACGTAGTTAAAGGTATTA

upper sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G02300.1 (Arabidopsis thaliana), 3'ss of exon 9
gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagatatggcttagctgatggactaatttaa--tcttaacttgaatgcctgttacctaagatatgtcttagctaatagactaatttaatctttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACTGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
                                                 |   ||      |   | |||  ||  | |||| ||  |  |||   |  |||   |   |  ||    |    ||    |      |||  ||||||||||||||||||||| | ||||| || ||||||||||| |||||| ||  |||    |||||||| |||||    || ||| |  | | ||   | |
------------------------------------------------gtaagttcttcttttctccaatcaaaacttttaaattaga--ccttccaagtaaacaaaagcacagaacctgagatagaaaatgtgaaaatctcagGATGGTTACTTCAAGATCAGGAGAGGAACGAACGAATGTGGCATTGAACAGAGTGTTGTAGCTGGTTTACCTTCAGAGAAGAACGTATTTAAAGGTATTA

upper sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 9
gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagatatggcttagctgatggactaatttaatcttaacttgaatgcctgttacctaagatatgtcttagctaatagactaatttaatctttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACTGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
                                                            | |     ||  |||     |||||||  |||| ||   |  | |||||   ||  ||     |  | || || ||| ||||||||||||||||| ||||||||||||   ||| || ||||| || |||||||  ||   |||||||||||||||  |||||||| |  | |  |  |   
----------------------------------------------------------gtaagattctatacaattcccccttgaattactgtcacaagaagtttgtctcgactcttaacactacatcattttgaatggcagGATGGTTACTTCATGATCCGAAGAGGAGTAAATGAGTGTGGCATCGAAGAGGGCGTGGTTGCTGGTTTGCCTTCTTCCAAAAACTTGATGATTGGAGACT

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:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|9258700|gb|BE346847.1|BE346847
EST:     CTTCTTGCTAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAA
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAA
EST: gi|7692402|gb|AW760509.1|AW760509
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|21675978|gb|BQ628329.1|BQ628329
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|7925196|gb|AW831222.1|AW831222
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTC
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTC
EST: gi|192322841|gb|FK014772.1|FK014772
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|254320265|gb|GR831073.1|GR831073
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|192312976|gb|FK003642.1|FK003642
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|6914718|gb|AW396248.1|AW396248
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAGGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|10252856|gb|BE820622.1|BE820622
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|192312975|gb|FK003641.1|FK003641
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|16282781|gb|BI945202.1|BI945202
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|254320264|gb|GR831072.1|GR831072
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|31476328|gb|CD418356.1|CD418356
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|209724788|gb|BW672571.1|BW672571
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|19346981|gb|BM891861.1|BM891861
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|14259461|gb|BG882369.1|BG882369
EST:     CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
EST: gi|208044091|gb|GD842853.1|GD842853
EST:     TGGCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT                         GATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG
genomic: TGGCTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGATgtatgtttct ... ttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctgttacctaagatatgtcttagctaatagactaatttaatctttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACTGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA
                                          tcttt  CT-rich tract
                          taatagactaatttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttcttgaattattcttcaacttgaatgcctgttacttaagatatggcttagctgatggactaatttaatcttaacttgaatgcctgttacctaagatatgtcttagctaatagactaatttaatctttaattgcagGATGGTTACTTCAAGATCCGAAGAGGGACAAACGAATGTGGGATTGAAGAGGATGTAACTGCTGGTTTGCCTTCCACCAAAAACCTCGTCAGAGAGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG