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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagactgttattatatcatgatatggtttttgtatgttgatcaacggaagacagcattgtgaagcttctgtttcaacttgtacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG

Basic information

species Zea mays
transcript GRMZM2G010823_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
gtaagcagactgttattatatcatgatatggtttttgtatgttgatcaacggaagacagcattgtgaagcttctgtttcaa---cttgtacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
      ||||||| |||  ||  ||||   ||||  || | |  || | |     || |   | | |||| |  |||| ||   |||  |  || ||||| |||||||| || ||||||||||||||  |||| ||||||||||| |||
---gtaagactgt-attgcatt-tgatt--gtttcagtttctcaattagc-----actgtgctatcaagcattggttttaactacttccatcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 11
-----------gtaagcagactgttattatatcatgatatggtttttgtatgttgatcaacggaagacagcattgtgaagcttctgtttcaacttgtacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
            ||     |||     ||  | |    |    || | | ||     |||  | ||   | | | | ||||  |    | |   |||    |||||||||| ||||| || ||||||||||||||| |||| ||||| |||||||||
accaatcatttatatttttactagggataagttagacaacaccttctatgtgccttacaattggagtttg-actct-aagccacaaccttattctgt----ttcagGGGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 11
---------------------------------gtaagcagact-gttattatatcatgatatggtttttgtatgttgatcaacggaagacagcattgtga---agcttctgtttcaact-tgtact-tttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
                                  ||  || ||  ||| || | |  |    | | | | ||   ||| |  |     |  |  ||||  |     ||       ||||| | | || ||||||||||| ||||| || ||||||||||||||| |||||||||| ||||| |||
gtaagatcctcatgctgactgaatttaaatttgttacacaaaccagttgttttcttttttacttgctatagttcattgttttatttttgttacaattggaatttgactctaagcacaactgtattctgtttcagGGGAAGGTTAACCCTACCCAGTGTGAGGCTTTGACAATGGTGTGTGCCCAG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 11
-------------------------------------gtaagcagactgttattatatca--tgatatggtttttgtatgttgatcaacggaagacagcattgtgaagcttctgtttcaact-tgtact-tttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
                                       || |   ||||| |  | |||  || ||| |||  |  || ||  |   |     |  | | | |||  ||   |   ||||| | | || ||||||||||| ||||| || ||||||||||||||| |||||||||| ||||| |||
gtaagatcctcatgctgactgaatataaatttgttacacaaaccagctgttttcttgtcacttgctatagttcattaat-ttatttgtcttgcaattggaatttgactctaa-gccacaactgtattctgtttcagGGGAAGGTTAACCCTACCCAGTGTGAGGCTTTGACAATGGTGTGTGCCCAG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagcagactgttattatatcatgatatggtttttgtatgttgatcaacggaagacagcattgtgaagcttctgtttcaacttgtacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
||| | |  |  |  |  | |  |  | ||   |||   | || |  |            ||     |  || | | ||         || ||||||||| || ||||| || |||||||||||  |||| |||||||||||||||
gtatgaatgcaatcttcctttgctcttctgtccttttctttttcactagttttgattcaaat----gaatttttatctc--------tttctcagGGGAAGGTAAATCCTACACAGTGTGAGGCCTTGACTATGGTTTGTGCACAG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 9
-------------gtaagcagactgttattatatcatgatatggtttttgtatgttgatcaacg------gaagacagcattgtgaagcttctgtttcaacttgtacttttc----agGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
              |||    | | || ||   ||||       ||  |||      |  || |        |   |  ||| ||    ||   |||||  |    ||| |     |||| || || |||||||| ||||||||||||||||| ||||| ||||| |||
gtgagttctttacctaaaaccattcttttttgttcatttctaatttcctgttgacaaagaaaggctttttatatttaatattctgggagttaattttcatgtatagcttctattcgagGGAAAGGTCAATCCAACACAGTGTGAGGCTCTGACTATGGTCTGTGCTCAG

upper sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 12
------------------gtaagcagactgttattata-tcatgatatggtttttgtatgttgatcaacggaagacagcattgtgaagcttctgtttcaacttgtact-tttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
                        | | | |||| | | | |  | ||| | |||  |  |  |    |   |   || |||       |  |  || | ||| | || |||||||| || ||||| || || |||||||||||||| |||||||| ||||| |||
gtaaaatcctgatctctttcccatatatttttatgacagtaaaaagatgatattttcacttgcacttgctacatttaggattcatttattcatcctttagctttttctatttcagGGAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG

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|60342181|gb|DN209154.1|DN209154
EST:     TTGGTGAACTAATCCTACCAGAAAATGAGCCTGGGAGCAGCATTATGCCT                         GGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
genomic: TTGGTGAACTAATCCTACCAGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagcagac ... tacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
EST: gi|5901092|gb|AW042192.1|AW042192
EST:     TTGGTGAACTAATCCTACCAGAAAATGAGCCTGTTTTTAGCATTATGCCT                         GGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
genomic: TTGGTGAACTAATCCTACCAGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagcagac ... tacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG

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: 245

TGGTCCTCGGTGTGGTCTTGGTGAACTAATCCTACCAGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagcagac ... tacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 420

TGGTCCTCGGTGTGGTCTTGGTGAACTAATCCTACCAGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagcagac ... tacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

TGGTCCTCGGTGTGGTCTTGGTGAACTAATCCTACCAGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagcagac ... tacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 311

TGGTCCTCGGTGTGGTCTTGGTGAACTAATCCTACCAGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagcagac ... tacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgatcaacggaagacagcattgtgaagcttctgtttcaacttgtacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG
 tgttgat  putative branch site (score: 311)
                                             tacttttc  putative PPT
                                             tactttt  TA-rich tract