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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttcagaaccttcacattctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagattaatttatttataggaaactaaccttgtattccatactttgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG

Basic information

species Glycine max
transcript GLYMA14G01290.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 6
gtaagcatttcagaaccttcacattctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagattaatttatttataggaaactaaccttgtattccatactttgtgc-catagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG
         | || |   |    || ||||         |  | |    || |||| | ||  || |     |   || |||  |     ||||| |||||    ||  |    || |       |  |||||| || |||||||||| || ||||||||||| ||||| || || ||||||||||| |||||||| || || || ||||| ||| ||||||| || || || || |||
--------gtaagtagtgttttgttttactatagcatatttgaaaacctatatatagactttatatcc----tccaaagtatttttcccgtaattcatttactaaaacat----ttatgccttg-atcttgtgcacacagAACTGCAAGATACACCATTCTGTAGTTGGACTCCGTTCTTGCATATCTGAAGGTGCTATCATAGAGGACACTTTACTAATGGGTGCGGACTACTATGAG

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 6
gtaagcatttcagaaccttcacattctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagat-taatttatttataggaaactaaccttgtattccatactttgtgc-catagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG
             || |    | || |||||    ||    |  |  |  ||| || | |||||    |   | || ||  ||||      ||||| |||||    ||  |    || |       |  |||||| || |||||||||| ||  |||||||||| ||||| || |||||||||||||| |||||||| || || || ||||  ||| ||||||| || || || || |||
-----------gtaagcagtgc-ttttactg--tagcatatttgaaaacctttctatacttctt--ttattttctccaaagtaatttctcataattcatttactaaaacgt----ttatgccttg-atcttgtgcacacagAACTGCAAGATAAACCATTCTGTAGTTGGACTCCGATCTTGCATATCTGAAGGTGCTATCATAGAGGACAGTTTACTAATGGGTGCGGACTACTATGAG

upper sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 6
gtaagcatttcagaaccttcacat-tctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagattaatttatttataggaaactaaccttgtattccatactttgtgc-catagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG
|||||     ||    |   |||  |||  || | || |   ||  ||     | |   || ||||  || | | |  |  ||  |  ||||| |  | ||| || ||  |  ||||||   || |  | |||||    ||||||| ||||| || ||||||||||| ||||| ||||||||||||||||| ||||||||||| ||||| ||  |||| ||||| ||||||||||| |||
gtaagttacacatgggcaagacaggtctcttgctgtgtttcatagttgg----tgtcacatgcttatgaaggctttttataattgtt-gatta-tgcagtta-agtaagtt--ccttgttcacccttttctgtgcatgcagAACTGTAAAATCCATCATTCTGTGGTAGGGCTCCGATCTTGCATATCAGAGGGTGCAATTATAGAAGATACACTATTGATGGGAGCAGATTATTATGAG

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|120494929|gb|EH223096.1|EH223096
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGNCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|209712746|gb|BW681600.1|BW681600
EST:     AAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: AAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|31472397|gb|CD414425.1|CD414425
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGTTGAAGAATGTGTGATTAAG                         AACTGCGAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|22522873|gb|BU081684.1|BU081684
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|15287005|gb|BI470896.1|BI470896
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|10238679|gb|BE807567.1|BE807567
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|17518996|gb|BM188038.1|BM188038
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|31468241|gb|CD410269.1|CD410269
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGNTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|31461779|gb|CD403807.1|CD403807
EST:     ATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: ATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|192295337|gb|FG985991.1|FG985991
EST:     GGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: GGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|51335512|gb|CO979378.1|CO979378
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|10232477|gb|BE801365.1|BE801365
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|5770728|gb|AI973902.1|AI973902
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|7640498|gb|AW734799.1|AW734799
EST:     TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: TTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
EST: gi|22929307|gb|BU546446.1|BU546446
EST:     ATGTGTGATTAAG                         AACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA
genomic: ATGTGTGATTAAGgtaagcattt ... tgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagattaatttatttataggaaactaaccttgtattccatactttgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG
                      aactaac  putative branch site (score: 1)
     ttaatttatttatagg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatttcagaaccttcacattctactgatctgctctgtacatgagatttatacaattcttaacaaagatgtcaaatataatgagattaatttatttataggaaactaaccttgtattccatactttgtgccatagAACTGCAAAATTCACCATTCTGTGGTTGGGCTGCGATCTTGCATATCAGAAGGTGCAATTATTGAAGACACGTTATTAATGGGGGCAGATTATTACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT