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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttaaattgggtgtattcacgttcttgcactgcttattttgataaaatcctaagagcttgctgaagacgatacgtgctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG

Basic information

species Zea mays
transcript GRMZM2G165535_T05
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os04g58580.2 (Oryza sativa), 3'ss of exon 5
gtaagcttaaattgggtgtattcacgttcttgcactgcttattttgata-aaatcctaagagcttgctgaagacgatacgtgctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
            || |  | ||   ||| | |   ||||| ||   | | ||||  ||||  | |||    || ||||| || ||||| |||||||||||||||||||| ||||||||||||||||||||||| |||||||| |||||
-----------gtgagccttttttagttatagtgttgcttgttcacacataaattttaaggccatgcaatcgatgatacatgttctttgcagGAATTTATTAACTTCACGCTTCATTACATTGCTGACTTGGACATCCCAATCAAAAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA09G39800.1 (Glycine max), 3'ss of exon 6
---------gtaagcttaaattgggt-gtattcacgttcttgcactgctt-attttgataaaatcctaagagcttgctgaagacgatac--gtgctctttc-cagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
         || |  || |||    | ||   ||  |           || || |  ||||| ||||      ||  | | |||   |    || | || | ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| ||||| ||
taactacttgtgaaattcaataaaattgtgggcatataaagaaggcattttatatcaataaattcct-----tttaataatgacagaattgatgatgttccgcagGAGTTTATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGAG

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G46390.1 (Glycine max), 3'ss of exon 6
----------gtaagcttaaattgggt-gtattcacgttcttgcactgctt-attttgataaaatcctaagagcttgctgaagacgatac--gtgctctttc-cagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
          || |  || |||   || ||   ||  |           || || |  ||||| |||     | ||  | | |||   |    || | |    ||||| ||||||||||| || |||||||| |||||||| ||||| ||||| ||||| | 
ttaactacttgtgaaattcaataaagttgtgagcatataaagaaggcattttatatcaataaactcc-----gtttaataatgacagaattgatgatatcctgcaGGAGTTTATTAACTTTACACTTCATTATATTGCTGATTTGGACATCCCCATTAAGA-

upper sequence: GRMZM2G165535_T05 (Zea mays), 3'ss of exon 6
lower sequence: Vv15s0046g03520.t01 (Vitis vinifera), 3'ss of exon 5
-gtaagcttaaattgggtgtattcacgttct-tgcactgcttat--tttgataaaatcctaagagcttgctgaagacgatacgtgct------ctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
 ||   |  | ||  | || |  |||   |  |||| |||  ||  ||    | |   ||      ||  ||     |||  ||          | | |||||| ||||||| ||||| |||||||| ||||||||||||||||||||||| |||||
agttctccaacatctgttg-acacacacacaatgcattgcaaatggttgtgcagacgtctgttcatttattgtttttgatgtgttacaaatgattgtgcagGAAATTATTAATTTCACACTTCATTATATTGCTGACTTGGATATCCCAATAAAAAG

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|6020771|gb|AW065579.1|AW065579
EST:     TGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTAANTTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAA
genomic: TGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTT-A-TTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAA
EST: gi|78118501|gb|DV536885.1|DV536885
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|40334667|gb|CK368737.1|CK368737
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTATATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|32919710|gb|CF024522.1|CF024522
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTATATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71763428|gb|DR961365.1|DR961365
EST:     TTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: TTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71771666|gb|DR969603.1|DR969603
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|148950412|gb|EC895979.2|EC895979
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|14646044|gb|BI180233.1|BI180233
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|148943663|gb|EC888727.2|EC888727
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|148947648|gb|EC893128.2|EC893128
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|148943662|gb|EC888726.2|EC888726
EST:     AGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|76280415|gb|DV019983.1|DV019983
EST:     AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|71299718|gb|DR785869.1|DR785869
EST:     AAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: AAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
EST: gi|76280414|gb|DV019982.1|DV019982
EST:     CCAAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAG                         GAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT
genomic: CCAAAGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATT

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: 49 (upstream exon), 49 (downstream exon)
Score: 123

AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 328

AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 199

AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG


Block sizes: 49 (upstream exon), 36 (downstream exon)
Score: 320

AGTTTGAAATCATTTATCGGAGAAGACAAGCTGAAGgtaagcttaa ... ctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttattttgataaaatcctaagagcttgctgaagacgatacgtgctctttccagGAATTTATTAACTTCACTCTTCATTACATTGCTGACTTGGATATCCCAATTAAAAG
     ttttgat  putative branch site (score: 320)
                                           tgctctttcc  putative PPT
     ttttgataaaat  TA-rich tract