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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattagctggcaaaaaattagatatacatttgcaattgacttttttttcccccctctagagagactcaggtaaaatatagtggttccaaccttgatgtatcttgtggctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG

Basic information

species Glycine max
transcript GLYMA20G38030.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G027282_T01 (Zea mays), 3'ss of exon 6
gtattagctggcaaaaaattagatatacatttgcaattgacttttttttcccccctctagagagactcaggtaaaatatagtggttccaaccttgatgtatcttgtggctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG
           || |  ||  | | | | ||   |||| |||| |     |     ||        |  |  |    |      | | ||  ||  | | | ||     | | | ||||||||| ||||| || ||||| || ||| |||||||||| |||||||| || ||||||||||| |||||||| |||||  |||| |||
-----------catacgatgtgttctcctttactaattaacttgtgagcacaattgct-------ttttgtgagtgcaagagtctcctaatatttttctttgtttcattttactacagTGAAGTTAGTGGTGATAGAGAAGTGCAAAGGACAATGTTGGAATTGCTGAACCAGCTTGATGGATTTAGCAGCGATGAGAGGATAAAG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 6
gtattagctggcaaaaaattagatatacatttgcaattgacttttttttcccccctctagagaga---ctcaggtaaaatatagtggttccaacc-ttgatg-tatcttgtggctga-ttgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG
                                                | | |  |||||||  |   |  |  ||   |||  |  |||  |    | ||| |  ||| |   ||  || ||| ||||| ||||||||| | ||||| ||| |||||||||| ||  |||| || ||||||||||| || ||||| ||||| || ||||||
-----------------------------------------------gtactctatctagagtcatgtcataactattttattttctttctgatgactaatgctgacttttaattggcttacagCGAAGTTAGTGGAGACCGTGAGGTACAAAGGACAATGTTGGAGCTGCTCAACCAGCTTGATGGATTCAGCAGCGATGATCGCATTAAG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 6
gtattagctggcaaaaaattagatatacatttgcaattgacttttttttc--------ccccctctagagagactcaggtaaaat-----atagtggttccaaccttgatgtatcttgtggctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG
   | | |    |     ||||   ||||| |   || ||  ||||| ||               |  |   |   |||| || |       ||        ||  |    | |  ||    | ||||||||||||| |||||||| || ||||| || ||||||||||| || ||  | |||||||||||||| |||||||||||||| || || |||
--gtaaaccattattggtttagcactacatctttcat-gatatttttatcaaaatggatttggattgaaattatcaaggtgaactcatgagcagcctccttgactatagacttttctgccttttattgcagTGAAGTGAGTGGAGATAGGGAGGTGCAGCGGACAATGTTGGAGTTATTGAATCAGCTTGATGGCTTTAGCAGTGATGATCGCATAAAG

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|298189083|gb|HO037486.1|HO037486
EST:     ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
EST: gi|208207319|gb|GE002158.1|GE002158
EST:     A-TATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTCAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
EST: gi|208192404|gb|GD988796.1|GD988796
EST:     ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTCAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
EST: gi|7233106|gb|AW568456.1|AW568456
EST:     ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
EST: gi|192327046|gb|FK015213.1|FK015213
EST:     ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATCGCTTAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
EST: gi|192317514|gb|FK008966.1|FK008966
EST:     ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
EST: gi|208335595|gb|GE137586.1|GE137586
EST:     ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTCAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
EST: gi|298174321|gb|HO017657.1|HO017657
EST:     ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAG                         TGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA
genomic: ATTATTTTTATAGATGAAATTGATGCAATTGGAACCAAGCGTTTTGATAGgtattagctg ... ctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactcaggtaaaatatagtggttccaaccttgatgtatcttgtggctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG
                                           ggctgat  putative branch site (score: 4)
        taaaatatagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattagctggcaaaaaattagatatacatttgcaattgacttttttttcccccctctagagagactcaggtaaaatatagtggttccaaccttgatgtatcttgtggctgattgcagTGAAGTAAGTGGAGACAGAGAGGTCCAACGGACAATGTTAGAATTGCTTAATCAGCTTGATGGTTTTAGCAGTGATGACCGGATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT