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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagggggctggggaagaatcatagtgttcaatggagggaatgagatgtgtttttgggaagaggtttcttattattgaatctaattgtgttatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGTTTACCAGTCCTTGTGTTGTGGGGCATGAGATTACCGGTGAGGTTGTTGA

Basic information

species Glycine max
transcript GLYMA08G00740.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G00740.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G63620.2 (Arabidopsis thaliana), 3'ss of exon 1
agagggggctggggaagaatcatagtgttcaatggagggaatgagatgtgtttttgggaagaggtttcttattattga-atctaattgtgttatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGTTTACCAGTCCTTGTGTTGTGGGGCATGAGATTACCGGTGAGGTTGTTGA
                   || |  | |||   |||    ||   ||   ||| | |||   |  || | |   ||   ||  | ||  |||   | | ||| |||||||| |||||||||||||| ||||| |||||||| || || |||||  | |||||||||||| | || ||||||||||| ||||| ||||||||
--------------gttcttcttcattttctg-ggatttgattgaatcaatttgtaggattcgagttttgaaagttagtattcattttcgtttgtgggcagCTTGTGGAGTTTGCCACTCTGATCTTCATGTGATGAAAGGAGAGATACCGTTCGCTAGTCCTTGTGTTATTGGTCATGAGATTACTGGTGAAGTTGTTGA

upper sequence: GLYMA08G00740.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g03150.t01 (Vitis vinifera), 3'ss of exon 1
agagggggctggggaagaatcatagtgttcaatggagggaatgagatgtgtttttgg-------gaagaggtttcttattattgaatctaattgtgttatgg-------tgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGTTTACCAGTCCTTGTGTTGTGGGGCATGAGATTACCGGTGAGGTTGTTGA
              | |||||  ||| || |   | |||| |    | |  | ||         ||| |        |  | |||  ||   ||  || |||       || ||||||||||||||| ||||||||||| |||||||| ||||| ||| |||| ||| | || |||||||| |||||||| ||||| || ||||||||||||||
------------aaaggaatc--agtctttatatgcgggattctcttttcctcttcttctatctgaaaaaagcctagaacaatgacactggctgaattttggaattaaatgcagCCTGTGGAGTATGTCACTCTGATCTGCATGTTATCAAAGGAGAACTTCCATTTGCTAGCCCTTGTGTGGTGGGGCACGAGATAACGGGTGAGGTTGTTGA
















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|298177589|gb|HO027256.1|HO027256
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|254329030|gb|GR833402.1|GR833402
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|192294197|gb|FG986286.1|FG986286
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|209714515|gb|BW684878.1|BW684878
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|298178116|gb|HO027499.1|HO027499
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|24137030|gb|BU927540.1|BU927540
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|192331064|gb|FK020284.1|FK020284
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|298172796|gb|HO020350.1|HO020350
EST:     ACTTCACATGCCCCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|192330970|gb|FK023125.1|FK023125
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|254330134|gb|GR839687.1|GR839687
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|298169952|gb|HO018576.1|HO018576
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACACTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|298189802|gb|HO038205.1|HO038205
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCA
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCA
EST: gi|192294016|gb|FG987185.1|FG987185
EST:     ATTTCGCATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
EST: gi|4396346|gb|AI495343.1|AI495343
EST:     ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGG                         CCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT
genomic: ATTTCACATGCCTCGCCCCAAGGCCGGTGAAGTTCTCATCAAAACAAAGGgtaagggtac ... tatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgtttttgggaagaggtttcttattattgaatctaattgtgttatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGTTTACCAGTCCTTGTGTTGTGGGGCATGAGATTACCGGTGAGGTTGTTGA
                                 atctaat  putative branch site (score: 3)
                   tttcttattattgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagggggctggggaagaatcatagtgttcaatggagggaatgagatgtgtttttgggaagaggtttcttattattgaatctaattgtgttatggtgtagCCTGTGGAGTATGCCACTCTGATCTACATGTTATGAAAGGTGAAATTCCGTTTACCAGTCCTTGTGTTGTGGGGCATGAGATTACCGGTGAGGTTGTTGA

- - - ggctggg
- - - - - - - - - - - -agtgttc
- - - - - - - - - - - - - - - - tggaggg