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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaataatgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC

Basic information

species Glycine max
transcript GLYMA09G36130.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G36130.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
gaaaaagctccttttaaagcacagtaaatacatgct--tgattcttgtcaattaataatgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC
                       || | | ||| ||  | | | |  |   ||   |  |   ||  |     || | |  |     ||  ||  | |||||||||| ||||||| ||||| |||  |||  |  ||||||||||| |  | ||| |||| |||||||||||||||||||| |||||||| ||||| |||||
-----------------------gttagttcattctattaactttatttggtttccatcggtctgaagtcctgtgctaatgccaaccttcctt--tttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC

upper sequence: GLYMA09G36130.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G162251_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------------------------------gaaaaagctccttttaa--agcacagtaaatac--atgcttgattcttgtcaatt---aataatgtattgttggtaaatggtgagactgttgttggttcat--atgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC
                                                                                          |  ||||   ||||    ||||  || |      | |  | |   ||||| | |   |   ||| | |         || ||  | | |      ||||    |||||||||| ||||||| ||||| |||  |||| |  | ||||||||  |  ||||| ||||||||||||| ||||||||||| || ||||| || || |||||
gtatgcactgaagcactatttacttatcttaatattttattcatcatgcaacccctttattaactcttcttttctcctggcaccatgtaaatgaagcagattttggacagcaaggtcagcgtcaacgaatcaactttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC

upper sequence: GLYMA09G36130.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G162251_T02 (Zea mays), 3'ss of exon 4
gaaaaagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaataatgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC
             | |  |  ||   |||  |  |||  |     || ||  ||    |    | | |  ||| | |         |     || |||||||||| ||||||| ||||| |||  |||| |  | ||||||||  |  ||||| ||||||||||||| ||||||||||| || ||||| || || |||||
------------gtcagcgt-caacgaatcaa--ctttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactat-tgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC

upper sequence: GLYMA09G36130.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G30700.1 (Arabidopsis thaliana), 3'ss of exon 5
gaaaaagctccttttaaagcacagtaaatacatgcttgat---tcttgtcaattaataatgtattgttggtaaatggtga-gactgttgttggttcata-------tgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC
        ||  || |   || | |  | |  || |||||   | ||||    |    |      |||   || || | | ||   || |||| | | |       | |||| ||| | ||  ||||||  |||| |||  |||||||||| ||  |||||||||  |||||||||||||||||||  || ||||||||||| || |||||
-gtttgcatcaattcatctcatattccaaagttgtttgatatgtgttgttgtctcgccagaataagttaaaaagtgttaatgatcttttttgggtaacaatgtgattatagGTTGTCTTCTGAGAAGCTATCCTGCAGACTTGATATTTGATAACACATCAGGCTACAGCTTTACATGTGATTTGACAGACAACATTGCTGCTCCATGGCC

upper sequence: GLYMA09G36130.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0094g00050.t01 (Vitis vinifera), 3'ss of exon 3
-gaaaaagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaataatgtattgttggtaaatggtgagactgttgtt-ggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC
   |  | ||||||| |||   |  |   |   ||  ||   |   | || || |  | |     ||   ||       ||||| ||  |||| | ||| ||| ||| |||||||||||||||||| |||||||   |||||||||||| ||||||| |||||||| ||||| ||||||||||| ||||| || || |||||
tccagtaactcctttgaaaatgccatgttttagtgtatg--ccaaattaaatatttgtttgggtctgtagaagaaatgaactgtggtcaggtttaaatgcagGATGTCTACTTCGAAGCTTGCCTGCAGATGTGGACTTTGACAATTCAACAGGCTTCAGCTTTACGTGTGACTTGAGTGATAATATTGCAGCTCCATGGCC

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|193534220|gb|FK488661.1|FK488661
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193342463|gb|FK306093.1|FK306093
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCT
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCT
EST: gi|207796620|gb|GD770782.1|GD770782
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193349410|gb|FK314118.1|FK314118
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193697924|gb|FK640591.1|FK640591
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193344938|gb|FK311564.1|FK311564
EST:     AGCATACAAGCTTATGGACAACAAG                         GACTGTTTACTTCGAAGC
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagG-CTGTTTACTTCGAAGC
EST: gi|193401830|gb|FK367063.1|FK367063
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193459852|gb|FK422631.1|FK422631
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|207790491|gb|GD760438.1|GD760438
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|208218018|gb|GE016106.1|GE016106
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|207764181|gb|GD737996.1|GD737996
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193623436|gb|FK576830.1|FK576830
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGA
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGA
EST: gi|193385721|gb|FK349403.1|FK349403
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|207790232|gb|GD762713.1|GD762713
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGC
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGC
EST: gi|208303795|gb|GE105264.1|GE105264
EST:     CTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: CTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|207748224|gb|GD721783.1|GD721783
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGA
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGA
EST: gi|193446954|gb|FK416215.1|FK416215
EST:     ACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: ACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|208308615|gb|GE104507.1|GE104507
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193493960|gb|FK461816.1|FK461816
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|208283644|gb|GE082400.1|GE082400
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|208314527|gb|GE113863.1|GE113863
EST:     AGCATACAAGCCTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193557069|gb|FK516170.1|FK516170
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193512649|gb|FK466389.1|FK466389
EST:     GCATACAAGCTTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: GCATACAAGC-TTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|208185609|gb|GD986252.1|GD986252
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193726807|gb|FK662779.1|FK662779
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193415992|gb|FK376654.1|FK376654
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|207696743|gb|GD677004.1|GD677004
EST:     TTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: TTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
EST: gi|193334835|gb|FK298443.1|FK298443
EST:     AGCATACAAGCTTATGGACAACAAG                         GCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG
genomic: AGCATACAAGCTTATGGACAACAAGgtttgctctt ... tcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattaataatgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC
  aattaat  putative branch site (score: 3)
     taataatgtattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaataatgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - -agctcct
- - - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgttg