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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaacatatactttgttaattatatgtgttaatgtttttgcgaaattattactaacaaagcgtgattagttcagcgatttaacctttgtagtaat...

Basic information

species Zea mays
transcript GRMZM2G059151_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 3
AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaacatatactttgtta--attatatgtgttaatgtttttgcgaaattattactaacaaagcgtgattagttca-gcgatttaacctttgtagtaat
|||   |  | |||||||||| |||||||| ||||||||  |||||||||||||||| || || |||||| | || | |||||| ||||||||||| |||||| |||||| || | |   | |  ||  |||  | |      || |  |  |   || |  |  |   |   ||  ||| |  | || |  |  || ||   
AGGATCCGTCATGTATGGATTCAAGGGAGGTCCAGCTGGAGTCATGAAGTGCAAGTACGTTGAGCTCACTGCGGATTATGTGTACCCCTACAGAAACCAGgtatagcaacttagattcactaagcatgctattgggtcgaaaattcgacaggtgcctattctctgattttctgtaaatcatgttagtttag-taggtggtg--

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G39380.1 (Glycine max), 5'ss of exon 3
AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaacatatactt----tgttaattatatgtgttaatgtt----tttgcgaaattatta--ctaacaaagcgtgattagttcagcgatttaacctttgtagtaat
||| ||||| |||||||| || | ||| || |||||||| |||||||||||||| || || ||||| || ||||||| | | ||||| ||||||||||||||  |    | ||||  |    | || |    || | |||   ||    |||   |  |||||   || |   |   | |||| ||      ||  | ||          
AGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTATATTTATCCTTACAGAAATCAGgtttattttcctataagtgtagttttgacacaatatattacctttattttttttaattttattgttcttatggaaatttattacttgtatatttggagct----------

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0059g01220.t01 (Vitis vinifera), 5'ss of exon 3
AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaacatatacttt-gttaattatatgtgttaatgtttttgcgaaattattactaacaaagcgtgattagttcagcgatttaacctttgtagtaat--
 || |||||| |||||||||| ||||| ||||| |||||||||||||| ||||| ||||| ||  | || || || ||| |   ||| | | |||| |||||        | ||  ||| | |   | || |||||  ||| |   |    ||  ||  ||| |  |   |||         ||| ||     ||  ||||  
GGGAAGCACCATGTATGGATTCAAGGGGGGCCCTGCTGGGATCATGAATTGCAAATATGTTGAGTTGACATCGGAGTTTATCCTTCCTTTCCGAAACCAGgtgagtttttaaatgtttttggttgctttaggtgtttgtgtgtc-acatgcttgata--aacgattcaacattgtcatgataattcaaaaacagtgctaataa

upper sequence: GRMZM2G059151_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 5'ss of exon 3
AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaacatatactttgttaattatatgtgttaatgtttttgcgaaattattactaacaaagcgtgattagttcagc-gatttaacctttgtagtaat-
||| |||||  ||||||| || ||||| || || |||||||||||||||||||| ||||| ||||||   || || ||| | ||||| || |||||||||||   ||    | ||   | | | || ||  |  ||||||   |  |    ||| |   |     |     |  |||| |  | || |  ||    |  |  
AGGAAGCACACTGTATGGGTTCAAGGGTGGTCCCGCTGGGATCATGAAGTGCAAATATGTTGAACTCGACTCTGAATTTATCTATCCTTATAGAAATCAGgtgaggctttctttag--tataatttgtagtttctaatgtaaatcagctgctatcaaatatttttcaactatttttcatctaaattgaggttgactgagact

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|29167975|gb|CB411235.1|CB411235
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211458486|gb|FL255599.1|FL255599
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACTAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|149083748|gb|EE173108.2|EE173108
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|148953762|gb|EC899129.2|EC899129
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211336169|gb|FL255577.1|FL255577
EST:     GCTAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAA-TCAC                         GGTGGATCTGAT
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGAT
EST: gi|211458479|gb|FL255592.1|FL255592
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211458477|gb|FL255590.1|FL255590
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211334013|gb|FL255572.1|FL255572
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCG
EST: gi|5268364|gb|AI770328.1|AI770328
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACCAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211462254|gb|FL324872.1|FL324872
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211179440|gb|FL364368.1|FL364368
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211540563|gb|FL329390.1|FL329390
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|149083929|gb|EE173306.2|EE173306
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211187935|gb|FL314087.1|FL314087
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211458484|gb|FL255597.1|FL255597
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211523118|gb|FL350158.1|FL350158
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAA
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAA
EST: gi|211414893|gb|FL345683.1|FL345683
EST:     GCA-GTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GTTGGGATTTGATATGATCTGCAGTGG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGG-ATTTGATATGATCTGCAGTGG
EST: gi|211336170|gb|FL255578.1|FL255578
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GNTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACGGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|211458364|gb|FL364597.1|FL364597
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|149103124|gb|EE288493.2|EE288493
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|20803238|gb|BQ294288.1|BQ294288
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|31354738|gb|CD439095.1|CD439095
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|148963458|gb|EE014477.2|EE014477
EST:     CAAGTATGTAGAAACTCACTTCAAACTTTGTGTATCCCTACAAAAATCAG                         GGTGGATTTGATATGATCTGCAG
genomic: CAAGTATGTAGAA-CTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAG
EST: gi|211334009|gb|FL255568.1|FL255568
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
EST: gi|149105648|gb|EE291200.2|EE291200
EST:     GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAG                         GGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG
genomic: GCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 327

AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 302

AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 303

AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 294

AGGCAGCACCTTGTATGGATTTAAGGGAGGCCCAGCTGGGATCATGAAGTGCAAGTATGTAGAACTCACTTCAGACTTTGTGTATCCCTACAGAAATCAGgtacagcaac ... ctcttgatagGGTGGATTTGATATGATCTGCAGTGGAAGGGACAAGATTGAAACACCGGAGCAG