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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttatttatggcttgaggatagcacatgaacgattgaagttgtttatctggtgatgttttttgttttttctgtgggtgtaaaccttgacctggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG

Basic information

species Glycine max
transcript GLYMA16G03170.1
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------tttatttatggcttgaggatagcacatgaacgattg-----aagttgtttatctggtgatgttttttgtttttt-----ctgtggg---tgtaaaccttgacctggttt-ttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
                                                              ||  ||  | ||  | |               |||        |  |    ||| | ||  |||| |   |||      ||  ||   ||||   ||| |      |  ||||| |||||| |||||  ||||||||||  ||||||| || ||  | || |||||| |||||||||| |||||| | | ||||||||||||||| ||||| |
gtatccttcaaatttattatttggtgacttcttgttgggtttcaactctagcctaccccaacttgcttgggactaaaaggctatgttgatgttgttgtcttttgatcatcctcctgcttattattttggcactttaagcattggcggcattgtatctcttaataaatctccttagACCAACAAGGACATCATTGCACAAATCGTATCTGCAAGTATCACGGGTGATATTATTCTTGCTGCTGCATATTCCCGTGAGCTGCCACGATACGGTCTAG

upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G163081_T04 (Zea mays), 3'ss of exon 3
tttatttatggcttgaggatagcacatgaacgattgaagttgtttatctggtgatgttttttgttttttctgtgggtgtaaaccttgacctggt--ttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
      |||   ||||  ||   ||      | ||  |  | ||  | ||||  | |    |       |      ||||   ||| ||  | |  | ||||| |||||| |||||   ||| ||||| ||||||||||| || || || ||||| ||||||||| | || ||  | |||||| ||||||||||||||||||
-----gtatcctttgattatttgaccatctggtttctacctattgctatggtactttgagctccagaagcatatattgtatctcttaactagatattcttagACCAACAAGGACATCACTGCCCAAATCATATCTGCTAGTATAGCGGGTGATATGGTTCTTGCTTCTGCCTACTCGCATGAGTTGCCACGATATGGTCTTG

upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G815894_T03 (Zea mays), 3'ss of exon 3
-----------tttatttatggcttgagga--tagcacatgaacgattgaagttgtttatctggtgatgttttttgttttttctgtggg-------tgtaaaccttgacctgg--tttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
           ||  || ||   |||      | |  | | ||  ||     || |   | |    ||| |  |||   |  | ||||        ||||   ||| ||  |   |  ||||| |||||| |||||    |||||||| || |||||||| || || || ||||| ||||||||| | || ||  | |||||| ||||||||||||||||||
gtatcctttgattccttcatcatttgttttctttgttctttaatcatctggtttctgcttattactatggtacttgagctc-cagtggcataatattgtacctcttaactagacctccttagACCAACAAGGACATCACAGCACAAATCATCTCTGCTAGTATAGCAGGTGATATGGTTCTTGCTTCTGCTTACTCGCATGAGTTGCCACGATATGGTCTTG

upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0094g00870.t01 (Vitis vinifera), 3'ss of exon 3
----tttatttatggcttgaggatagcacatgaacgattgaagttgtttatctggtgatgttttttgttttttctgtgggtgtaaaccttgacctggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
     ||| || |  |        |    |||| |  |||  |||  |||||||   | |  || |||  | |   |   || ||||||| |||| |||  ||||  ||||| || ||| |||| ||||||| ||| |||||||||||||| ||||| || |||||| | |||||| | |||||||| || |  ||||| ||||
ctgggttacttttttccctctttcaatg-atgagct-ttgttgtttgttatctgccaa-gcattctgtgctgttgatctttg-aaaccttaaccttgttactagACTAACAAGGATATTATTGCCCAAATAACATCCGCTAGCATTGCTGGTGATATAGTCCTTGCTTCTGCATATTCTCATGAGCTACCTCACTATGGACTTG

upper sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 4
-tttatttatggcttgaggatagcacatgaacgattgaagttgtttatctggtgatgttttttgttttttctgtgggtgtaaaccttgacctggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
 ||| | | || | |   | | | |  |      |||  | |   ||     | ||  | ||| ||||| || |   |||||||||| ||    || | |||  ||||| || ||   ||| ||||| ||||||||||| |||||||| ||||| |||||||| || || ||| | ||||| ||||| |  ||||| ||||
atttttatttgacatatag-ttgaaggtcttattttgggggtaaatagacaatcatactgtttctttttcctctttttgtaaaccttaacactattctcagACGAACAAGGATATAACTGCTCAAATTATATCTGCTAGTATTGCTGGTGATATGGTTCTTGCAGCGGCCTATTCCCATGAACTGCCTCACTATGGGCTTG

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|7041875|gb|AW471769.1|AW471769
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|21602194|gb|BQ612525.1|BQ612525
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|4436984|gb|AI522849.1|AI522849
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|192315894|gb|FK008595.1|FK008595
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGTTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|13252441|gb|BG363352.1|BG363352
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|15336852|gb|BI497508.1|BI497508
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTTTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|4397465|gb|AI496462.1|AI496462
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|19268986|gb|BM885242.1|BM885242
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|192308475|gb|FK001377.1|FK001377
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|209701098|gb|BW664200.1|BW664200
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|192317627|gb|FK007581.1|FK007581
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGTTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|7233168|gb|AW568517.1|AW568517
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|151393465|gb|EV263340.1|EV263340
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAAC-AAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|18040030|gb|BM308324.1|BM308324
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|7284984|gb|AW597471.1|AW597471
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|15814259|gb|BI786534.1|BI786534
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|192315893|gb|FK008594.1|FK008594
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGTTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|151412354|gb|EV282166.1|EV282166
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|42722855|gb|CK768754.1|CK768754
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT
EST: gi|192317628|gb|FK007582.1|FK007582
EST:     AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTC                         AGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGTTGGCGAT
genomic: AGGACAAGAACAAATATAACACCCCGAAATATCGCTTTGTTGTTCGTTTCgtatcctttt ... tggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctggtgatgttttttgttttttctgtgggtgtaaaccttgacctggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG
                                   aaccttgac  putative branch site 
                                                ttttt  putative PPT
        atgttttttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttatttatggcttgaggatagcacatgaacgattgaagttgtttatctggtgatgttttttgttttttctgtgggtgtaaaccttgacctggtttttagAGCAACAAAGACATTGTTGCACAAATAATATCTGCTAGCATTGCTGGCGATATTGTTCTTGCTGCAGCATATGCACATGAGCTGCCACGATATGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - tggcttg
- - - - - - - - - - - - catgaac
- - - - - - - - - - - - - - - - - - - - - - - tctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttgac