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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacactaacattaagaataaaccaaacttgttcag

Basic information

species Glycine max
transcript GLYMA13G23790.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g29180.1 (Oryza sativa), 5'ss of exon 5
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGg-----tattttaaatttctatagcactagctt-gcccttttttacctaagtt------atttcacttggtggaacactaacattaagaataaaccaaacttgttcag
||| |||||||| || ||||| ||||||||||| |||||||| |||||||| || ||||||||||| |||||||| ||||| || || || ||||||||||     | || || || | |    |  || ||| |  | ||    | |||  |      || | | |  ||||   ||   ||  | |  | ||| |||||       
TGTCTGGTTCCCCCAACCAGCACCAAAGGATCACCCATGGCGATACATGCCTAATCATGCCATGACCCCTCATATCTCTGGGACTACAATTGATGCACAGgtcagcttttatatatgttttctactttaacttagggcattggagcataaaattctagaatctgattctgtggg-tacccccacaatgctttaacaaaact-------

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g29220.1 (Oryza sativa), 5'ss of exon 6
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacactaacattaaga---ataaaccaaacttgttcag------
 || |||||||| |||||||| ||||||||||| |||||||| |||||||| || ||||| ||||| |||||    ||||| || || || |||| ||||||      |  ||||||    |   ||  | || ||| |   ||    |    | |        |     ||  |||   || |     | ||  |         
CGTCTGGTTCCCCCAGCCAGCACCAAAGGATCACCCATGGCGATACATGCCCAATCATGCTATGACCCCTCACTGCTCTGGGACTACAATTGATGGACAGgtc-----agcttctatgtttcctactctctctatttaaaaaaaaacttaaatcctaaaaatgaatctgtatctagatttatcatttggatttaattccttttgg

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G049811_T01 (Zea mays), 5'ss of exon 5
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgt--attttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacactaa-------cattaagaataaaccaaacttgttcag
||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| || || || ||||| |||||    ||   | || | |  |   || |||    | |  | |||| || |   || |  | | ||||||        | | | | || | |  ||||   |   
TGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTACAATTGATGCGCAGgtcaggttctgagttttgttacctgagtttgaaaatct--atctaa-ttctaatacctcataggacactaggtctctgcttcatgcattagcagaactcaata--

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G147714_T01 (Zea mays), 5'ss of exon 6
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgt--attttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacactaa-------cattaagaataaaccaaacttgttcag
||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| || || || ||||  |||||    ||   | || | |  |   || |||    | |  | |||| || |   || |  | | ||||||        | | | | || | |  ||||   |   
TGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTACAATTGATGAGCAGgtcaggttctgagttttgttacctgagtttgaaaatct--atctaa-ttctaatacctcataggacactaggtctctgcttcatgcattagcagaactcaata--

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G418005_T01 (Zea mays), 5'ss of exon 4
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgt--attttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacactaa-------cattaagaataaaccaaacttgttcag
||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||| | || || || ||||| |||||    ||   | || | |  |   || |||    | |  | |||| || |   || |  | | ||||||        | | | | || | |  ||||   |   
TGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTAGGACTACAATTGATGCGCAGgtcaggttctgagttttgttacctgagtttgaaaatct--atctaa-ttctaatacctcataggacactaggtctctgcttcatgcattagcagaactcaata--

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G423972_T02 (Zea mays), 5'ss of exon 4
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgt--attttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacactaa-------cattaagaataaaccaaacttgttcag
||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||| | ||||| || ||||| || || || ||||| |||||    ||   | || | |  |   || |||    | |  | |||| || |   || |  | | ||||||        | | | | || | |  ||||   |   
TGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGGCCCCTCACATCTCTGGGACTACAATTGATGCGCAGgtcaggttctgagttttgttacctgagtttgaaaatct--atctaa-ttctaatacctcataggacactaggtctctgcttcatgcattagcagaactcaata--

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G362021_T01 (Zea mays), 5'ss of exon 7
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgt--attttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacacta-------acattaagaataaaccaaacttgttcag
      ||||||| ||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| || || || ||||| || ||    ||   | || | |  |   || |||    | |  | |||| || |   || |  | | ||||||       || | | | || | |  ||||   |   
------GTTCCCATAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATATCTGGGACTACAATTGATGCGCATgtcaggttctgagttttgttacctgagtttgaaaatct--atctaa-ttctaatacctcataggacactaggtctctacttcatgcattagcagaactcaata--

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 5'ss of exon 5
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaatttctatagcactag--cttgcccttttttacctaagttatttcacttggtggaacac-taacattaagaataaaccaaacttgttcag
||||||||  ||||||||||| || ||||| ||||||||||| |||||||||||||| || ||||| ||||||||||||||||||||||| ||||||||||||    || ||||||     ||    ||| || |    ||  |  | | ||    |   || ||| | ||| ||    |||    |||  |||| |||
TGTTTGGTATCCACAGCCAGCCCCCAAGGACCATCCATGGCGGTACATGCCAAACCAAGCTATGACCCCTCATATTTCTGGCACCACCATTGATGCACAGgtaccc-aagtttctacttttcttctccttcccttcccgtatttttgcttttctcatgcttgtaactcataaaatggccaatgggacaatattgtgcag

upper sequence: GLYMA13G23790.3 (Glycine max), 5'ss of exon 6
lower sequence: PP1S106_16V6.2 (Physcomitrella patens), 5'ss of exon 8
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaatttcta-----tagcactagcttgcccttttttacctaagttatttcac---ttggtggaacactaacattaagaat---aaaccaaacttgttcag---------------------
||| |||  | | ||||| ||   |||||| ||||| |||||||||||||| ||||| |||||||| || ||||| || ||||| ||| | || || |||||  |  ||  | |       ||| | ||   |  |  | || |  |     ||| ||    ||    ||    | | ||  | |||   | |  || | |  |||                      
TGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGACCCTCGACGCCCAGgtgatgaaagctccccaccattaggattacagtatcagtcttaatttcctgcattgcaagcattatcagaggcttcatatctataattccagaaaaatcctactcataaattcctcctcctcttgcag

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|11275020|gb|BF325344.1|BF325344
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|17401257|gb|BM178039.1|BM178039
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|42723252|gb|CK769151.1|CK769151
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACT
EST: gi|6454580|gb|AW185263.1|AW185263
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|42723150|gb|CK769049.1|CK769049
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|214008422|gb|DB989988.1|DB989988
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|42723195|gb|CK769094.1|CK769094
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|22927396|gb|BU544535.1|BU544535
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|4260047|gb|AI416543.1|AI416543
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|15199628|gb|BI423928.1|BI423928
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACCTTATGCCGCTGGGCCCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|6341426|gb|AW164250.1|AW164250
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAATACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|18735405|gb|BM528746.1|BM528746
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|11688868|gb|BF596544.1|BF596544
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|11274460|gb|BF324813.1|BF324813
EST:     ATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: ATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|18038684|gb|BM306978.1|BM306978
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|11688173|gb|BF595849.1|BF595849
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATTCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|209715917|gb|BW650930.1|BW650930
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|26060128|gb|CA803042.1|CA803042
EST:     AAACCATGCCATGACTCCTCATATTTCTGGCACCCCCATAGATGCACCAG                         T-ACGTTATGCTGCTGGGGGCCAAGACCTGCTTGATAGGCACTTCAAG
genomic: AAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCAC-AGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAG
EST: gi|13790807|gb|BG653398.1|BG653398
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
EST: gi|6200999|gb|AW153099.1|AW153099
EST:     CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAG                         TTACGTTATGCTGCTTGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT
genomic: CAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaa ... acttgttcagTTACGTTATGCTGCTGGGGTCAAAGACATGCTTGATAGGCACTTCAAGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCACCATAGATGCACAGgtattttaaatttctatagcactagcttgcccttttttacctaagttatttcacttggtggaacactaacattaagaataaaccaaacttgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC