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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggtttttgttgcagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG

Basic information

species Glycine max
transcript GLYMA17G29080.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g39720.3 (Oryza sativa), 3'ss of exon 2
------cggtttttgttg--cagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
        || | | | |  ||||  |  ||  ||  ||   | | | |||  |  ||| |       |       | |||    | | |  | | |  | | |||||||| ||||||||  | | |||||| |||| ||| ||||||||||||||||||||||| |||||| | ||||| || ||||| || ||||
aattcatagtctatatggagcagtaatgatttcttaattatgtctgcaaatgagattatct------gattcttccactttcaactgagt--tgtttcttctatgcagTGTATGGGTTGCTAGAAAACCACCAGGTTTTGCCTTTATTGACTTTGATGACCGCAGGGATGCAGAAGATGCAATTCGTGATTTAGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g54770.1 (Oryza sativa), 3'ss of exon 2
----cggtttttgttgcagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
    |     |   |  ||||||      ||||  | |   | || | || |  ||    | |       |||| |  | || ||   ||| || |   |||||||| |||||||| |||| ||||||||||| ||| ||||| || |||||||||   || |||||  |||||||  ||||||| || ||||
tattcctgactcaatatagtggtaccc-cttgtactataagt-tatttggac-gttgcgggtatgtttgttgatgtaattttcaagtgtatttt-tccatgcagTGTCTGGGTTGCCCGTAAACCACCTGGTTTTGCATTTATCGATTTTGATGACAAGAGGGATGCTGAGGATGCACTCCGTGATTTAGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027105_T02 (Zea mays), 3'ss of exon 2
--cggtttttgttgcagtggtttttat-ttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtt--tgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG-----------
   |   | | ||| | |   |   || |   ||| ||| |  ||||| |     | ||  |    | ||| |||    |  | || | |||| | |   |||||||| ||||||||  | | |||||| || | ||| || |||||||||||||||||||| |||||||| ||||| || |||||||||||||           
caagaaatgtattgaactcaataccatatcactttttttgtacaatagat-----tattatagtttatatgctttcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATGGTACTTAATAA

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G070239_T02 (Zea mays), 3'ss of exon 2
cggtttttgttgcagtggtttttatttgttttgtttttctaataggtct---attttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
        | || || |||||| || |||| | ||| | ||  |  |||    || |  ||  || |  || |   ||     |     |||| |   |||||||||||||| ||||| | ||||||||||| ||| |||||||| ||||| ||| | || |||||| |||||||||| |||||  | ||||
--tagcgagatggagaggtttt-atctgttatatttctttacgacttctttcgttatcagatgaacacctggtgcagtccactaactgttgttctcaatgcagTGTTTGGGTCGCACGCAAACCACCTGGTTTTGCATTTATTGATTTTGACGACAGGAGGGATGCAGAGGATGCTATTCGTGATCTAGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G070239_T04 (Zea mays), 3'ss of exon 2
cggtttttgttgcagtggtttttatttgttttgtttttctaataggtct---attttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
                   |||||| |||| | ||| | ||  |  |||    || |  ||  || |  || |   ||     |     |||| |   |||||||||||||| ||||| | ||||||||||| ||| |||||||| ||||| ||| | || |||||| |||||||||| |||||  | ||||
------------------gttttatctgttatatttctttacgacttctttcgttatcagatgaacacctggtgcagtccactaactgttgttctcaatgcagTGTTTGGGTCGCACGCAAACCACCTGGTTTTGCATTTATTGATTTTGACGACAGGAGGGATGCAGAGGATGCTATTCGTGATCTAGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G027105_T06 (Zea mays), 3'ss of exon 1
--cggtttttgttgcagtggtttttat-ttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtt--tgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
   |   | | ||| | |   |   || |   ||| ||| |  ||||| |     | ||  |    | ||| |||    |  | || | |||| | |   |||||||| ||||||||  | | |||||| || | ||| || |||||||||||||||||||| |||||||| ||||| || |||||||||||||
caagaaatgtattgaactcaataccatatcactttttttgtacaatagat-----tattatagtttatatgctttcacttggactgatttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGACCGCAGGGATGCACAAGATGCCATTCGTGAATTGGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G080930_T01 (Zea mays), 3'ss of exon 2
-cggtttttgttgcagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
  ||||||  |||  | |   |||   | |||| ||| | |   || |  | ||| |      |    |     ||   |||   | |||| |   |||||||||||| ||||||||| ||||||||| | ||| |||||||| ||||| ||| | || |||||  |||||||||| |||||  | ||||
taggttttacttgttgcgtcctttgcgttttttttttctttgtgagatggagtttgttgtttcacctggtgcaggtcgctaactgt-tgttctcaatgcagTGTTTGGATTGCACGTAAACCACCTGGCTTTGCATTTATTGATTTTGACGACAGGAGGGATGCGGAGGATGCTATTCGTGATCTAGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G107896_T01 (Zea mays), 3'ss of exon 2
-cggtttttgttgcagtg--gtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
  ||| ||     || |    |    | |  |||| | | |  ||||| |   | | ||  | |   | | | || |    | ||  | |  | |   |||||||| ||||||||  | | |||||| || | ||| || |||||||| ||||||||||| |||||||| ||||| || || || |||||||
aaggtattgagctcaataccataccaaatgtttttttctctacaatagattattgtattttatatgcattcacttgga--ctgat-ttgttctttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTCGATGACCGCAGGGATGCACAAGATGCCATTCGCGATTTGGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G31580.1 (Arabidopsis thaliana), 3'ss of exon 2
-cggtttttgttgcagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgttt----aatgct-atgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
       |   | || |   |    || |   |    || |   |  | |    ||  ||||  |    ||||||  | |    |||| | || |    | ||||||||||||||||| ||||||||||||||||| |||||| | || || || || |  || ||||| |  |||||||||||||  || ||||
gtaagaatcaatccaatcaatca-gttcgcgctacaattttgtcacttttgaagtt--aaaagtatccaattttgcatctctctaatgttcatatgtaatgtgcagTGTTTGGGTTGCCCGTAGACCACCTGGTTACGCTTTTCTAGATTTCGAAGATCCTAGGGATGCCCGTGATGCTATCCGTGCTTTAGATG

upper sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 2
--cggtttttgttgcagtggtttttatttgttttgtttt-tctaataggtctatt-ttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
    |||||||||  ||  ||||  | |       ||   || | || |       |||| |    | |||  || |   |||  ||  ||||| | | |||||||| ||||||||||| |||||||| || ||||||||||| |||||||||||||| ||||||||||| ||||| || |||||||| ||||
ttaagtttttgtttaag--gtttggagtaacaccattgagtccattatgcaggcaatttttatttcagaat--ttcttaattttctgaaatgttttatgtgcagTGTCTGGGTTGCACGCAGACCACCAGGCTATGCTTTTATCGACTTTGATGACCGTAGAGATGCACAAGATGCAATTCGTGAATTAGATG

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|298194616|gb|HO043088.1|HO043088
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCCGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298195473|gb|HO043864.1|HO043864
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGCAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|193574368|gb|FK527921.1|FK527921
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTG
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTG
EST: gi|16996813|gb|BM086185.1|BM086185
EST:     ACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|192298779|gb|FG991015.1|FG991015
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|151398824|gb|EV268695.1|EV268695
EST:     ACCGAGAGAGACCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298193289|gb|HO033723.1|HO033723
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|254339463|gb|GR848221.1|GR848221
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|58020796|gb|CX707538.1|CX707538
EST:     GAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: GAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|6566908|gb|AW234540.1|AW234540
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|20498854|gb|BQ273784.1|BQ273784
EST:     GTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: GTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|151393372|gb|EV263247.1|EV263247
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTACGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|192294144|gb|FG986233.1|FG986233
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|254344199|gb|GR855284.1|GR855284
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|15814312|gb|BI786587.1|BI786587
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|254344200|gb|GR855285.1|GR855285
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|151410968|gb|EV280783.1|EV280783
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG
                              gtttaat  putative branch site (score: 4)
     ttttttgaaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggtttttgttgcagtggtttttatttgttttgtttttctaataggtctattttttgaaaaaaaaatgattttgtgtttaatgctatgttatgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGACCGCAGAGATGCACAGGATGCTATCCGTGAATTGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG