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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgtatgaactagtcgtttgaaaattgaaatgttgagcttactaactgccagttttggcatcatttgaatatttacagtaacgtatctcatgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG

Basic information

species Zea mays
transcript GRMZM2G054247_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 3'ss of exon 3
gctgtatgaactagtcgtttgaaaattgaa-atgttgagcttactaactgccagttttggcatcatttgaatatttacagtaacgtatctcatgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG
    | |       |    ||| | ||||| |  || |  || || ||||  ||| |||   | || | |  || |    || | | |||| |   |  |||| |||| ||| ||||||||| ||||||||||||| ||||| || ||||||||||| ||   |||||| ||
atgctcttgcaggatgaactgatacttgaacactttcaatttgctcactgatagtattgctttgatctaatgatgtgttata-cttttctcgtatctgtagGAAATTAAAACTGTGGAGCTTTCAAAGCCAGTTGGGTGGGTTCATATATCATTATCTGGAGCTGATCCCCG
















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|76915292|gb|DV165923.1|DV165923
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|60400666|gb|DN233473.1|DN233473
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|78088159|gb|DV516552.1|DV516552
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|13515650|gb|BG517926.1|BG517926
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|22490544|gb|BU050467.1|BU050467
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|71297609|gb|DR784753.1|DR784753
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|12045796|gb|BF727935.1|BF727935
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCT
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCT
EST: gi|71422983|gb|DR805911.1|DR805911
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|78180912|gb|DV551285.1|DV551285
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|16379595|gb|BI993037.1|BI993037
EST:     CGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|71297610|gb|DR784754.1|DR784754
EST:     CGCCGAGCAAGATCTTCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGTCAGTTGGATGGGTCCAC-TATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|91873253|gb|EB403210.1|EB403210
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|87153735|gb|DY398524.1|DY398524
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|149073064|gb|EE161334.2|EE161334
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|71427965|gb|DR809015.1|DR809015
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|211368075|gb|FL362342.1|FL362342
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATG--TCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|94476642|gb|EB705600.1|EB705600
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
EST: gi|71449488|gb|DR830538.1|DR830538
EST:     CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAG                         GAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA
genomic: CGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCA

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: 47 (upstream exon), 46 (downstream exon)
Score: 158

CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 223

CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 207

CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 230

CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGCAAGATCTCCATCCGGGCCGGGGATGGCTTCCACAACCTAAAGgtacgctttt ... atgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgccagttttggcatcatttgaatatttacagtaacgtatctcatgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG
               atcatttgaatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgtatgaactagtcgtttgaaaattgaaatgttgagcttactaactgccagttttggcatcatttgaatatttacagtaacgtatctcatgattccagGAGATTAGAACGGTGGAGCTTGCAAAGCCAGTTGGATGGGTCCACATATCATTATCCGGGATTGATCCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
-ctgtatg
- - - - - - - - - - - - - - - atgttga
- - - - - - - - - - - - - - - - - - - - - - -actgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatttg