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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttcagttactccatatggtacattaacttaaaaattttgagtgtgcaaaatatggcagttgtactgttcccttcattaaaacaatgctgtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC

Basic information

species Zea mays
transcript GRMZM2G133885_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133885_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 8
-------------------------------------------------------------------gtgtgttcagttactccatatggtacattaa--cttaaaaattttgagtgtgcaaaatatggcagttgtactgttcccttcattaaaacaatgctgtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC
                                                                   |  ||||| | | ||        | | ||||   ||       || |   |||| | | |    | | | ||  | | |||||| |  |||| |   |||   ||||||||||||||||||| |||||  |||| ||||||||||| |||||||| ||||| ||||| ||||| ||||||||||||||||||||||| || ||||
gtatgtttcagctaatccattagttagattaactgccattctctatttatgtgggcttattaacagagcttgttctggtccttttgggtctgctttaaggttttttctccttaaagttgcatattttaattgctctcct--ttctttcatttactcaatacatggatt--agGTTTTCGACCGGCGAACTAAGAGACTAGTTGAAGAAGTTATAGACGGAAAGATTGTGTTGTCTATGAGAGCTTTATACCAATCAAAAGTAGGGCTAACTC
















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|34391219|gb|CF384447.1|CF384447
EST:     CCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTG                         GTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAA
genomic: CCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTGgtgtgttcag ... gtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAA
EST: gi|30591314|gb|CD052310.1|CD052310
EST:     CCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTG                         GTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAA
genomic: CCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTGgtgtgttcag ... gtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAA

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: 46 (upstream exon), 49 (downstream exon)
Score: 153

GTGGATGTTCAAGCTCAGTGAATGGGCACATTTCTCCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTGgtgtgttcag ... gtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

GTGGATGTTCAAGCTCAGTGAATGGGCACATTTCTCCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTGgtgtgttcag ... gtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GTGGATGTTCAAGCTCAGTGAATGGGCACATTTCTCCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTGgtgtgttcag ... gtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

GTGGATGTTCAAGCTCAGTGAATGGGCACATTTCTCCACGTATGATGTTGGTTTGCACTCTGGCTCTACAGCTTCACATATTCTGgtgtgttcag ... gtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaaatatggcagttgtactgttcccttcattaaaacaatgctgtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC
                            ttcattaaaacaat  TA-rich tract