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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcacatgtccttttctatcagttttcttttcctattgattttacattactactgaaggtaaccttctgtgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTTCAGAACACAGACCCTCTTTCTGGCAACGAAGTGGACGATGCTGTGCAGT

Basic information

species Glycine max
transcript GLYMA12G35320.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G35320.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv19s0014g02660.t01 (Vitis vinifera), 3'ss of exon 7
-------gtatttcacatgtccttttc------tatcagttttcttttcctattgattttacattact-actgaaggtaacctt---ctgtgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTTCAGAACACAGACCCTCTTTCTGGCAACGAAGTGGACGATGCTGTGCAGT------
          |||||  |   |||||       | | | |     ||| | ||  |||||   | | | ||| | | |   |||   ||||||   ||||||  |||| ||||||||||||||||||||||||||| || ||||||| ||  | | ||  |||      |||| | | |||   || ||| |||  ||||      
agatttctcttttcattttctcttttaataccatgttaatggatattttcaataaattttcattcatttactaatgcttttcttgttctgtgtttgttagGTTGTCATCTACCACAAGGCCTTCCCCATGCCAGCACTGACATTCAAATTCAACAGCATGGAC------TCTGACCATGAATCAGATGATTCTGCACAGTTCATCT
















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|57575187|gb|CX548162.1|CX548162
EST:     GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
EST: gi|58019897|gb|CX706639.1|CX706639
EST:     GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
EST: gi|10238749|gb|BE807637.1|BE807637
EST:     GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
EST: gi|10845522|gb|BF068626.1|BF068626
EST:     GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
EST: gi|207737976|gb|GD715656.1|GD715656
EST:     GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
EST: gi|151394104|gb|EV263975.1|EV263975
EST:     TGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: TGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
EST: gi|193633517|gb|FK579225.1|FK579225
EST:     GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
EST: gi|193568733|gb|FK527086.1|FK527086
EST:     GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATT
genomic: GGTTATCAGTATCTGATGGTTACATTGCCACTGGTTCAGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATT
EST: gi|193460763|gb|FK427532.1|FK427532
EST:     AGAGACAAATGAG                         GTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT
genomic: AGAGACAAATGAGgtatttcaca ... tgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttcctattgattttacattactactgaaggtaaccttctgtgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTTCAGAACACAGACCCTCTTTCTGGCAACGAAGTGGACGATGCTGTGCAGT
                                aggtaac  putative branch site (score: 3)
                                      ccttctgt  CT-rich tract
         tattgattttacatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcacatgtccttttctatcagttttcttttcctattgattttacattactactgaaggtaaccttctgtgtggattagGTGTTCATATACCACAAGGCCTTCCCCATGCCAGCATTGTCATTCAAGTTTCAGAACACAGACCCTCTTTCTGGCAACGAAGTGGACGATGCTGTGCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG