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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG

Basic information

species Glycine max
transcript GLYMA18G02210.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                                 ||   |    || ||  | |  || |   | || | |    |  | |  |      || | |   |  | | | | | | ||      || ||   | |||  |     || ||||     ||   |||| || || || || || ||||||||  |||| || |||||||| ||||| || || || || ||||| ||||| |||||||| |||||||||||||| |
---------------------------------gtaccaaccata-tatcaaatcctttggctagcttttcgcattgaaacgtcgatattcttccggaaacttttttttatatataacctgataag--aactttggc-----ttttgtt-----ttcgtagCCCACCTCAATTGTCAGCTACAACCACTTGGGGAATAATGATGGCATGAACCTTTCCGCACCTCAAACATTCCGATCCAAGGAGATCTCCAAGAGCAATG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G071174_T01 (Zea mays), 3'ss of exon 1
--gtacattgttgttatactaatgtcatatcatgggtgttatt----tttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatat-gtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
      |   | || |||    | |      ||   |  |  |    || | || || ||| | |  ||  |||   |    || ||| ||| |||| |   | |||   ||  | ||| || |  | ||  | | ||    |  | |  | | ||   |      |||| || || || |  || |||||||||||||||||||| || || ||||||||||| || ||||||  |||||| ||||| || ||||||||||||| ||
gtacgtaccatcgtcatatatgtatatctctatatataatgctgggattaattaagataatttgtgtttgacat---tcaagaataatctatccatctttaaatattggaattattaaagattggcacattggataataaggtggatttgttttttcccg-----tagCCCACCTCAATTGCAAGCTACAACCATCTGGGAAACAACGACGGCATGAATCTCTCTGCCCCACAAGTCTTCCGGTCCAAAGAGATCTCCAAGAGCAGCG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G177461_T01 (Zea mays), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgat-tgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
|||||||  |  | || |  ||         |||  |    || |   | |  || | || ||  |||   |    || |||  |   |   |  |||  |   |  | | | | || | | |   ||  | |||     | |  ||||  || | |   |||| || || || | ||| |||||||| || |||||||||||||| ||||||||||| || ||||||  |||||| || || || ||||||||||||| ||
gtacattccttgtctattgctgg--------gggcctgggattaagatgaattatttgtctttcacat---tcaagaataatcga---actttattagcatatcagataatataaggtggattctttttttctttctttttttcgtgtttgtgctgtcgtagCCCACCTCAATTGCTAGCTACAACCACCTAGGAAACAATGATGGCATGAATCTCTCTGCGCCACAAGTCTTCCGGTCTAAAGAGATCTCCAAGAGCAGCG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaat-gagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                                                               ||      | |||      || |   |      |  | | | | |   |||||  |  || |   | | | ||  |  | |||  ||  | ||   ||||| || || || || || ||||||||  |||||||||| ||||| ||||| || || || || ||||| ||| | |||||||| ||||||||||||||||
--------------------------------------------------------------gtgggaacctagtatctctcttctat-taagatgaagtgtttttttggcaaatgacgttattgcaataactcttctatattttcattt--tcat--gcagCCCACCTCAATCGTGAGCTACAACCACTTGGGAAACAACGATGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagat-ttatatgtcaaaaatggagaaatgagttgattt--tttcaagtgttc-tgttgatgattg-acagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                                                                             |||||||||  ||    |  ||| |      |   |||||        ||  ||  |  || |||   ||| |||  ||| |    ||||| || || || || || ||||||||  |||||||||| || || ||||| || || || || ||||| ||| | |||||||| ||||||||||||||||
---------------------------------------------------------------------------gtacaatttatcaatgaaacctgatatccccccttcgaaatgtttttggcagacgacatacttacaataattcgtgtatatgttcatgcagCCCACCTCGATTGTGAGCTACAACCACTTGGGAAACAACGACGGCATGAACCTGTCTGCCCCTCAAACATTCAGGTCCAAGGAGATCTCCAAGAGCAACG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: AT4G39800.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                                                        | |  ||  | ||  |   ||   | |  | | |  | ||  |  ||| ||||| ||             ||| |||  |  | |||  ||||  || || | |||| || || || || || ||||| ||  |||||||||| ||||| ||||||||||| |||||||| || ||| | || ||||| |||||||| ||||| |
-------------------------------------------------------gtttgtttaacttgcgtatcaagttactctttcttgttactgaaaatatttgtcacaag---------actttggtttcattgattgtg-tgtttttg-tttatagCCTACTTCAATTGTGAGCTACAATCACTTGGGAAACAACGATGGAATGAATCTCTCAGCTCCACAGACTTTCAGATCTAAGGAGATCTCCAAAAGCAATG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                        |||||||   |   ||||   ||     ||| ||   |||  |      ||||| || | |||||| ||  |||  |||| | | || ||||                | || ||   |  || || || | ||||||||||||| || || || || ||||||||||||||||| ||||| |||||||| || ||||| |||||||||||||||||||| |||||||||||||| |
----------------------gtatatcatttttagcatttcctctgttgaaatttagaattttaa-----agtaaataagt-atgcat-gta-taggattatgtatgaataatga---------------tattgaaagatgatgatggtggt-gacagCCAACATCCATTGTGAGCTATAACCATCTGGGAAACAACGATGGCATGAATCTGTCTGCTCCTCAAACCTTCCGCTCCAAGGAGATCTCCAAGAGCAATG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggac-aatctatcctttgcatgttttgtaaaca-atttatgcatcgtgctaga-tttatatgt--caaaaatggagaaatga--gttgattttttcaagtgttctgttgatgattg------acagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
           | |   ||| |    |  ||||| |||       | | | ||   ||    | ||  ||   | |  || |||| |  |   |  | ||  | |  ||  | |||||   |  | ||  ||||   ||     |  |   |||  | ||  |     ||  |||      ||||||||| || || ||||| ||||||||| |||| ||||| ||||| |||||  | || || || ||||| ||||| |||||||| |||||||||||||| |
gtgagccaagtgcaatgtgtagaggaataaatgtaataaagcct-tctaacttgcgctgaatccaacttagaatgtctattttttttggattcaggtgtgtctagaactgaagtttatgctttgcgaagctggaatgattgctatgaaagctttgcactgaacccacaattgttggtgtgcacagCCAACGTCAATTGTTAGCTACAACCATTTGGGCAACAACGATGGAATGAACTTGTCCGCCCCTCAAACATTCCGTTCCAAGGAGATCTCCAAGAGCAATG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: EFJ27629 (Selaginella moellendorffii), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgt---tctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                                                                                                              |||||   |   |      |||||| | | | |   || ||   ||  |  |||||||| || || || || ||||| ||||| || ||||||||||| |||||||| || || || ||||| ||| | ||||||||||||||||||||||| |
------------------------------------------------------------------------------------------------------------gtaaaatctcgtttttctcgtatttttccgactctaaatccgtct-tgtcttccagCCAACCTCCATTGTCAGCTACAATCATCTTGGTAACAATGATGGAATGAATCTATCTGCGCCTCAAACATTCAGATCCAAGGAAATCTCCAAGAGCAATG

upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 6
lower sequence: EFJ37320 (Selaginella moellendorffii), 3'ss of exon 6
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgt---tctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                                                                                                              |||||   |   |      |||||| | | | |   || ||   ||  |  |||||||| || || || || ||||| ||||| || ||||||||||| |||||||| || || || ||||| ||| | ||||||||||||||||||||||| |
------------------------------------------------------------------------------------------------------------gtaaaatctcgtttttctcgtatttttccgactctaaatccgtct-tgtcttccagCCAACCTCCATTGTCAGCTACAATCATCTTGGTAACAATGATGGAATGAATCTATCTGCGCCGCAAACATTCAGATCCAAGGAAATCTCCAAGAGCAATG

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|6502144|gb|AW203517.1|AW203517
EST:     CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
EST: gi|19453629|gb|BM955039.1|BM955039
EST:     CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
EST: gi|11413502|gb|BF425513.1|BF425513
EST:     CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
EST: gi|11688725|gb|BF596401.1|BF596401
EST:     CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
EST: gi|19270872|gb|BM887128.1|BM887128
EST:     CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
EST: gi|6454183|gb|AW184796.1|AW184796
EST:     CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
EST: gi|207834410|gb|GD806311.1|GD806311
EST:     CCAAAATGAAATCCGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTG
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTG
EST: gi|13790045|gb|BG652636.1|BG652636
EST:     CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAG                         CCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT
genomic: CCAAAATGAAATCTGTGTTGGTTGATTTTCTTGTGGGGGCTGGTATCAAGgtacattgtt ... tgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG
                                       tgttgat  putative branch site (score: 4)
                    ttgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattgttgttatactaatgtcatatcatgggtgttatttttactaggacaatctatcctttgcatgttttgtaaacaatttatgcatcgtgctagatttatatgtcaaaaatggagaaatgagttgattttttcaagtgttctgttgatgattgacagCCAACATCTATAGTTAGTTACAACCATCTGGGAAACAATGATGGTATGAATCTCTCGGCTCCACAAACCTTCCGCTCCAAGGAAATCTCCAAGAGCAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA