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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATAGCTATGCATCATATATTGGGCACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcattttttttccctcccttttgtgataattgatagatgtgtatatactttgatgtgtgttgtttccatttggctagttcatgctcttctaccttcg...

Basic information

species Glycine max
transcript GLYMA18G17590.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 4
GTGATAGCTATGCATCATATATTGGGCACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcattt--------tttttccctcccttttgt--gataattgatagatgtgtatatactttgatgtgtgttgtttccatttggctagttcatgctcttctaccttcg
  |||||||||||||| |||||||||||||| ||  | |||| ||  ||| | |||||||| |||||||| ||||||||||| || ||||  |||||||||||   ||         || |  | |  ||| |||  | || |||| |  | ||| |  ||||  || ||  || ||   |||    |||  | ||||| |  |      
-GGATAGCTATGCATCCTATATTGGGCACTATCCAATGCTGGCATATTTTTCCATTGCTGAGAATGAATCAATTGGAAGAGAGCGTTACAATTTTATGCAGgtatgttaaaagcttattataacatgtcttctgtacggtagttgaaaattatgt-tggactt--atctggtttattaatattgatgtagaac-tgctcctaaaa-----

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
GTGATAGCTATGCATCATATATTGGGCACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcattttttttccctcccttttgtgataattgatagatgtgtatatactttgatgtgtgttgtttccatttggctagttcatgctcttctaccttcg-----
 |||||| ||||| ||||| ||||| ||||||||| | ||   || ||||||||||||||| || || ||||||||| ||||||||||||  || |||||||||    |  ||||    | |||    || | |       ||| | | |  |  | ||      |||  |||     | |  ||| |  | |   |  |     
-TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtg-acaaatctaca-gttcaagatttggatt--atgattctatgtttatttgattaggtgcgt

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 3
GTGATAGCTATGCATCATATATTGGGCACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcattttttttccctcccttttgtgataattgatagatgtgtatatactttgatgtgtgttgtttccatttggctagttcatgctcttctaccttcg-
 ||||||||||||||||||| |||| |||||||| |||||||  |  ||||||||||||||||| ||||| ||||||||||| |||||||  ||||||||||||   | | | |       |  |   ||    | |   | |  |  |  | |    ||      ||       |  | || | |       |  ||   
-TGATAGCTATGCATCATATGTTGGCCACTACCCCTTACTGGCGTATTTTGCTATTGCTGAAAACGAATCAATTGGAAGAGAGCGCTACAATTTTATGCAGgtttgctctatgtattatagtagttgtattgcagttttctttaaaattgttgtttaatgaacaaattgagaaaaggaatttaaggtatgatcatatttac

upper sequence: GLYMA18G17590.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S215_103V6.1 (Physcomitrella patens), 5'ss of exon 3
GTGATAGCTATGCATCATATATTGGGCACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcattttttttcc-ctcccttttgtgataattgatagatgtgtatatactttgatgtgtgttgtttccatttggctagttcatgctcttctaccttcg----------------------------------------------------------
  || || ||||| || ||||| |||||    ||  |  |||  ||||||||  |||||||||||||||| |||||| |||  |||||||  |||||||||||  |   | ||    ||   | ||    |  | ||   || ||||  | | |  || ||    |  |||| |||  |  || ||| |  | ||  | |                                                           
-GGACAGTTATGCCTCCTATATCGGGCATGCACCACTGTTGGCCTTCTTTGCAGTTGCTGAAAATGAATCCATTGGACGAGTGCGCTACAATTTTATGCAGgtgaacaatcttaatgctgtatgttacattgctagagtcatttgtaagt-cctgaatttgaacagggtccacttgcgtttttgatggttctttatatactccaagctgttcttggatcatcttgatattcacctcatctcgttcttgtgtgacttcag

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|151408566|gb|EV278374.1|EV278374
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|42722515|gb|CK768414.1|CK768414
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|193395678|gb|FK362231.1|FK362231
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTT
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTT
EST: gi|26046065|gb|CA783407.1|CA783407
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|193636233|gb|FK580756.1|FK580756
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|193702556|gb|FK635222.1|FK635222
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|31465662|gb|CD407690.1|CD407690
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|192326871|gb|FK015128.1|FK015128
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|193466054|gb|FK429781.1|FK429781
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|19453331|gb|BM954741.1|BM954741
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|207701517|gb|GD682846.1|GD682846
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|12690859|gb|BG157195.1|BG157195
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAA-NCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|13790432|gb|BG653023.1|BG653023
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|298166319|gb|HO009290.1|HO009290
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|193702771|gb|FK637845.1|FK637845
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|8283605|gb|BE021164.1|BE021164
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
EST: gi|13478641|gb|BG508037.1|BG508037
EST:     GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCA                         GAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA
genomic: GCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcatttt ... ttgttgtgcaGAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATAGCTATGCATCATATATTGGGCACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAggttcattttttttccctcccttttgtgataattgatagatgtgtatatactttgatgtgtgttgtttccatttggctagttcatgctcttctaccttcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc