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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcatattcgcctattttgttttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT

Basic information

species Glycine max
transcript GLYMA07G06590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 3
------------gttatcatattcgcctattttgttttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacc-----tgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT
              |  |   |||   |||| || |        ||   | | |    |||| ||  | | ||||      || |      || || ||| || || || || ||||||||||||||  |||| ||||| |||||||| || || |||||||| ||||| |||||||| || || |||
gtatagtattcctcttgccccttcaaatattgtggtagcctccttttggtttggttagctctattt-tgatggtgtgctatttgcaaatcgtgtagCGGGCAAGACAGACTATCGTGCCAGGATTCGCCTGATCAATCAAGACAAGAATAAGTACAACACTCCAAAATATCGATTTGTCGTGCGATTT

upper sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 3'ss of exon 2
-------------gttatcatattcgcctattttgttttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT
              ||   || |||     | | |||||    | |||  |  |      | | |   |     |  |    ||  || |||||||||| || || ||| | || ||||||||  |||||||||| ||||||||||| ||||||||||||||||| || |||||||| || |||
gtattgtactacatttccaatgttcattcttatagtttttgggttttcgtttgttcgctttttatggatttaatttctaaaattgtctacagAGGGAAAGACTGACTACAGGGCTAGGATTCGCCTGATTAATCAAGACAAGAACAAGTATAACACTCCGAAATATCGCTTTGTTGTGCGATTT

upper sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S38_329V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------------------------------------gttatcatattcgcctattttgttttg----tcatgttcaa---tgttgaatactctgttag---taacggtgattctgttacc--tgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT
                                                                                       |||   ||  | |  | ||| | || |    ||  | ||     |||||  |  |  |   |   | | ||||||   |||     |||||  || ||||||||||||||||| |||||||| |||| ||  ||||| |||||||| || ||||| ||||| ||||| | ||| || || |||
gtgagtgggtttggtttgtgtttgggcatggattgttttgagtgacttgtttgtttttatctttagagtgtttggaattcaattttggttggaatggtggtgtgtttagattagggtttctggctctgggttgttgcgtttttcggaggagctgagggtgatgtggttgttgatgcagCCGGTAAAACCGATTACCGTGCGAGGATTCGTTTGACTACCCAGGATAAGAACAAGTACAACACCCCGAAGTACCGTTATGTCGTGCGATTT

upper sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S364_3V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------gttatcatattcgcctattttgttttgtcatgttcaatgttga-atactctgtta-gtaacggtgattctgttacc------tgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT
                                                                                      |  |||        ||| |  | | | |||   || ||  ||    ||||  | | | | |||| |||          |||||  || |||||||||||||| || ||||| || ||||  | ||||||||||||||| || ||||| ||||| ||||| || || ||||| || 
gtgcggatttttttgtggcatttgtcaccctcactgtcgaagatccttgatcttgaatcttttctgtgtgtcgttggtacagagggttgtatcgctggggtttctcgttttaggttttctgctggtatttcttgttgcggatctgagattgtgtgcatggattatgcagCTGGTAAAACCGATTACCGGGCGAGGATCCGTTTGACCACTCAGGACAAGAACAAGTACAACACCCCGAAGTACCGTTTCGTCGTTCGTTTC

upper sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ31187 (Selaginella moellendorffii), 3'ss of exon 2
gttatcatattcgcctattttgttttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT
                 |   | ||||   | ||  |  |||||   ||       |    |  |    | | ||  |||||| || |||||||| || ||  || | || ||||  |||||||||||||||||||| ||||| ||||| |||||||| || |||||||||
----------------gtaacgatttggattcttggagcttgaaatttc-----acatttctcttcgcttcatctctagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT

upper sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17161 (Selaginella moellendorffii), 3'ss of exon 2
gttatcatattcgcctattttgttttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT
                 |   | ||||   | ||  |  |||||   ||        ||  |   |||         |||||| || |||||||| || ||  || | || ||||  |||||||||||||||||||| ||||| ||||| |||||||| || |||||||||
----------------gtaacgatttggattcttggagcttgaaatttc--------acattt-ctcttcgcttcatagAGGGCAAGACCGATTATCGGGCTCGGGTGCGCTTGACGAATCAGGACAAGAACAAATACAACACACCGAAGTACCGATTCGTCGTTCGCTTT

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|254340071|gb|GR858196.1|GR858196
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|9203772|gb|BE329996.1|BE329996
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|37996752|gb|CF808341.1|CF808341
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|10844117|gb|BF067454.1|BF067454
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|8282719|gb|BE020280.1|BE020280
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|10847099|gb|BF069865.1|BF069865
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAATTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|10845936|gb|BF068951.1|BF068951
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
EST: gi|15815279|gb|BI787554.1|BI787554
EST:     ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAG                         AGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA
genomic: ATCAAAAGCCTACTTCAAGAGATATCAAGTCAAGTTCAAGAGAAGAAGAGgttatcatat ... ttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT
                            tagtaac  putative branch site (score: 1)
                                        ttctgtt  putative PPT
               ttgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatcatattcgcctattttgttttgtcatgttcaatgttgaatactctgttagtaacggtgattctgttacctgcagAGGGAAAAACCGATTACCGTGCCAGGATTCGGTTGATTAATCAGGACAAGAACAAATATAACACTCCGAAATACCGATTTGTTGTTCGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC