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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggaaacaaatttagactatcaggaaagcagtttgtggaataaattcaactaatccgtgccccaatttttcttaggcatgtgattaggaattaatgctccccaatcttgatttattgtgtcatactgaagaatttgatatggatattatttgtcccttgcattaaactttatgcccttttttctcctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG

Basic information

species Glycine max
transcript GLYMA15G15960.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G15960.2 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G017089_T01 (Zea mays), 3'ss of exon 14
gtatggaaacaaatttagactatcaggaaagcagtttgtggaataaattcaactaatccgtgccccaatttttcttaggcatgtgattaggaattaatgctccccaatcttgatttattgtgtcatactgaagaatttgatatggatattatttgtcccttgcattaa-actttatgcccttttttctcctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG
                                                                                       |    |||| |  |   ||| ||    | |       ||  || |||     || ||||| |      |  | || ||| | |  || |     |||    ||||  |  ||| || ||||| ||| ||||||| ||||| ||||||||||||||||| || || |||   || || || || |||||||
---------------------------------------------------------------------------------------tgaagattatttgtagtcaagctaagctaa-------attgtggagacc---atgtggatgtgcagaatggcgtgtattcataagttgtcaatatttgaaacctg--tgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG

upper sequence: GLYMA15G15960.2 (Glycine max), 3'ss of exon 14
lower sequence: EFJ31158 (Selaginella moellendorffii), 3'ss of exon 16
gtatggaaacaaatttagactatcaggaaagcagtttgtggaataaattcaactaatccgtgccccaatttttcttaggcatgtgattaggaattaatgctccccaatcttgatttattgtgtcatactgaagaatttgatatggatattatttgtcccttgcattaaactttatgcccttttttctcctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG
                                                                                                                       ||  ||    | | ||      || || |           | || |  ||   | |  | |||   ||    ||   |||||| ||||| ||||| |||||||||||||||| ||| || ||||| ||||||||| | ||||| || || ||||| |
-----------------------------------------------------------------------------------------------------------------------gtaacaggaggtaaaacaacgcatcgaca-------agtgtagcttcgaatcatctaacgtttgcgct----gtatcagGTGATAATGGAAGCATCTGGTTCTGGGATTGGACGAGCGGCCATAACTTCCAGCAAACTCAAACCATCGTTCAGCCAG
















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|6070929|gb|AW100316.1|AW100316
EST:     TGGTTACTGGAG                         GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
genomic: TGGTTACTGGAGgtatggaaac ... ctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
EST: gi|254313964|gb|GR831593.1|GR831593
EST:     TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAG                         GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
genomic: TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAGgtatggaaac ... ctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
EST: gi|254319813|gb|GR829217.1|GR829217
EST:     TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAG                         GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
genomic: TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAGgtatggaaac ... ctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
EST: gi|21993683|gb|BQ785211.1|BQ785211
EST:     TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAG                         GTGA-AATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
genomic: TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAGgtatggaaac ... ctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
EST: gi|37994708|gb|CF806333.1|CF806333
EST:     TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAG                         GTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC
genomic: TATCATCAATGCAATGGCTGTCAATGAGGAGGGTGTGATGGTTACTGGAGgtatggaaac ... ctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatattatttgtcccttgcattaaactttatgcccttttttctcctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG
                          ctttatgccctttttt  CT-rich tract
                    attaaactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggaaacaaatttagactatcaggaaagcagtttgtggaataaattcaactaatccgtgccccaatttttcttaggcatgtgattaggaattaatgctccccaatcttgatttattgtgtcatactgaagaatttgatatggatattatttgtcccttgcattaaactttatgcccttttttctcctggttaaagGTGACAATGGCAGCATGTGGTTCTGGGATTGGAAGAGTGGTCATAATTTCCAGCAATCCCAAACAATTGTACAGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA