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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcctacatatagaatcataaattttcatttaatttaaagattccttcaatctaatataaaattgaacagtgcctaattgtacatttctacattttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCTACTGGTATTGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATTTAA

Basic information

species Glycine max
transcript GLYMA17G33050.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 7
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 8
gcctacatatagaatcataaattttcatttaatttaaagattccttcaatctaatataaaattgaacagtgcctaattgtacatttctacatttt------ttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCTACTGGTATTGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATTTAA
   |||     |  | |||||        |  ||||||||   | | || |    ||  | |   | | ||  ||||  |  ||||||    | |      | |||  |||||| |||||||| || ||||| ||||| ||||||||||| || || ||||| ||||| |||||||| |||||||||| |||||| |||||| | |
---tactgtctgtgtgataaaacgagtacttgtttaaagacaacgtgaaaccctgatggatt---ataatggttaatcttgaatttctgttatgtaaaatgtacagGAAGCTCCAGAAGGATCCTTCATCTTGCTTCACGGATGTGCTCACAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCA

upper sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 9
gcctacatatagaatca-taaattttcatttaatttaaagattccttcaatctaatataaaattgaacagtgcctaattgtacatttctacattttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCTACTGGTATTGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATTTAA
 |  |  | |    |   |   | ||  || ||| |||   |   ||| |    | ||  | ||    | | |   |  ||  |||| |   | ||| ||| |||| || |||||||||||| | || |||||||| |||||||| || || ||||||||||||||||| ||||||||||||||||| || |||||| | |
-caaaagtttgttcttgcttggtattgtttcaatataattttcatttccaggctaaattcacttctttaattcaagagagtttatttatttttgtttccagGCAGCCCCAGAAGGATCTTTTGTGTTGCTTCATGGCTGTGCTCACAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCA
















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|51336363|gb|CO980229.1|CO980229
EST:     TGATTGAAGATATAAAG                         TCANNNCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT
genomic: TGATTGAAGATATAAAGgttaggttgt ... attttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT
EST: gi|120492269|gb|EH220436.1|EH220436
EST:     ATTGAAGATATAAAG                         TCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT
genomic: ATTGAAGATATAAAGgttaggttgt ... attttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT
EST: gi|120491497|gb|EH219664.1|EH219664
EST:     ATTGAAGATATAAAG                         TCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT
genomic: ATTGAAGATATAAAGgttaggttgt ... attttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT
EST: gi|120530683|gb|EH258816.1|EH258816
EST:     ATCCCAAGACAGTTGGTTTGGATTTTGAGGGCATGATTGAAGATATAAAG                         TCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT
genomic: ATCCCAAGACAGTTGGGTTGGATTTTGAGGGCATGATTGAAGATATAAAGgttaggttgt ... attttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatctaatataaaattgaacagtgcctaattgtacatttctacattttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCTACTGGTATTGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATTTAA
                         gcctaat  putative branch site (score: 3)
                                      tttctacattttttc  putative PPT
      taatataaaattgaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcctacatatagaatcataaattttcatttaatttaaagattccttcaatctaatataaaattgaacagtgcctaattgtacatttctacattttttcagTCAGCTCCGGAAGGATCTTTTATCTTACTTCATGGATGTGCTCATAATCCTACTGGTATTGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT