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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttatatgtctgccgcgggtaggcaggtagctgagcagattgtcttgtaaatctacgtccttttcatttcaccaatctgtggcattgattctgttgcagGTTAATCACACAAAAAGGGCACTGCATAATTACCTCATAACAAAACTTTATAG

Basic information

species Zea mays
transcript GRMZM2G180335_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180335_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g69130.2 (Oryza sativa), 3'ss of exon 17
ctttatatgtctgccgcgggtaggcaggtagctgagcagattgtct-tgtaaatctacgtcc----ttttcatttcac-caatctgtggcattgattctgttgcagGTTAATCACACAAAAAGGGCACTGCATAATTACCTCATAACAAAACTTTATAG
       || | |  |  | |   |||  | |  |        | | ||||||| | |        ||    || ||     | |  ||  ||| |||  ||||||||||| ||||||||| |||  |||||||||||||| ||||| || ||||||||
-----agtggcagg-gaagctgaccagaaatcctaattatccatgtctgtaaatttcctcttggggttgctgttgcatgttctttaaggatttgtttcgcttgcagGTTAACCACACAAAACGGGAGCTGCATAATTACCTTATAACTAAGCTTTATAG
















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|78087100|gb|DV515493.1|DV515493
EST:     TCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTG                         GTTAATCACACAAAAAGGGCACTGCA
genomic: TCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTGgtatgagaga ... tctgttgcagGTTAATCACACAAAAAGGGCACTGCA




















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: 144

ACTTGAAATAGCAATTACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTGgtatgagaga ... tctgttgcagGTTAATCACACAAAAAGGGCACTGCATAATTACCTCATAACAAAACTTTATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

ACTTGAAATAGCAATTACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTGgtatgagaga ... tctgttgcagGTTAATCACACAAAAAGGGCACTGCATAATTACCTCATAACAAAACTTTATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

ACTTGAAATAGCAATTACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTGgtatgagaga ... tctgttgcagGTTAATCACACAAAAAGGGCACTGCATAATTACCTCATAACAAAACTTTATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

ACTTGAAATAGCAATTACAAAGTTGCTATTGAAGTCATATTACAATATTGTCAGGAAAAATGTGGAGGACTTCATACCAAAAGCAATTATGCATTTCCTGgtatgagaga ... tctgttgcagGTTAATCACACAAAAAGGGCACTGCATAATTACCTCATAACAAAACTTTATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtaaatctacgtccttttcatttcaccaatctgtggcattgattctgttgcagGTTAATCACACAAAAAGGGCACTGCATAATTACCTCATAACAAAACTTTATAG
                                      cattgat  putative branch site (score: 124)
                                            ttctgtt  CT-rich tract
                ttttcattt  TA-rich tract