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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcatatgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 11
------tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcat--atgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG
      | || ||||  |   |  |  | | |    || ||||  |  |  |||  ||     | ||||| | |||   |   |||||||| ||||  |  | |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||||
atcttattttcttcttggttgcagagtttt-tgatgtatttttatttac--agcaaac-----tgtacctataaaggaaaaagatgctgacctatttatctcctgtagGTAATGCAAGGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGTCTAATTGAG

upper sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G19450.1 (Glycine max), 3'ss of exon 12
--tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcatatgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG
   ||  ||     |||| |  ||    |  | ||  |   |   |    | | | ||      | |  ||  | |  |  ||| ||  |  ||| ||  ||||||||||| ||||||| ||||| ||||| |||||||| || || |||||||||||  |||||
gtcatcctttattccaac-ctccttcagatgtaagcataatttattct-tcaaaagtgcccagtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGGGAAGGAGCAACATGCCTCGTTGAG

upper sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA10G05090.1 (Glycine max), 3'ss of exon 11
------tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcatatgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG
       ||  |  ||        | |||   || |    |||  ||   ||      | ||  |   | |  ||  | |  |  ||| ||  |  ||| ||  ||||||||||| ||||||| ||||| ||||| |||||||| || ||||||||||||||  |||||
cctttagatcttcttccatggt-tacctcgagacatgtaatttattcttcaaa-----agtgcctggtcagaaaatgtgaagttttgagttgattgttctttccagGTAATGCAAGGTCTTGCCAAATCAATAGCTTGGGATGGAGAAGGTGCAACATGCCTCGTTGAG

upper sequence: GRMZM2G044237_T03 (Zea mays), 3'ss of exon 11
lower sequence: Vv08s0040g03320.t01 (Vitis vinifera), 3'ss of exon 12
tattgttctcagcaacgcatctctgtaccttagttttgctccctaagccgacactgttttacctgttaagttcatatgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG
 | |    |     | |    |  |   |||   |||   |  | |       |  ||    |   |  | |||  |  | ||  ||  | |  ||  ||||||||||  ||||||||||||| |||||||||||||| || || ||||||||||||||||||
aagtcagttggctcatgaggtttagaggcttgaatttctactattatggacagcctttgggtccaatctggtcagttcttaacaaatgtccttttttcagGTAATGCAGGGTCTTGCAAAATCAATAGCATGGGATGGAGAAGGAGCAACATGCCTAATTGAG

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|32934567|gb|CF039379.1|CF039379
EST:     AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCA                         GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|32835096|gb|CD974774.1|CD974774
EST:     AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCA                         GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|32928445|gb|CF033257.1|CF033257
EST:     AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCA                         GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCA                         GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|78543892|gb|DV621390.1|DV621390
EST:     AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCA                         GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|32833027|gb|CD972705.1|CD972705
EST:     AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCA                         GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCA                         GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA
genomic: AAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACA

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), 45 (downstream exon)
Score: 114

TGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 109

TGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 77

TGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG


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

TGACTGTGTTATTGCTATGGCAAGTGGGTTGTCTGGTTTATCTGGAATTCAAAGTCTTGATAGCATTGAGGCTCAACAGTTCCAAGCATGCCTAGATGCAgtaagtatta ... ttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccgacactgttttacctgttaagttcatatgctgacttattccttccttgtagGTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG
                               tgctgac  putative branch site (score: 45)
                                     cttattccttccttgt  CT-rich tract
         tgtttta  TA-rich tract