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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagcaatttgaatattgcattatttgcactgaatcatcaagattaggatataatattgattactaaccttgtattgatgctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA

Basic information

species Zea mays
transcript GRMZM2G145019_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145019_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g51250.1 (Oryza sativa), 3'ss of exon 2
gtatgtagcaatttgaatattgcattatttgcactgaatcatcaagattaggatataatattgattactaaccttgtattgatgctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA
|||||| ||||||  | |  || |  ||    ||| |   |       | | |||||| |||| | ||||||| ||| ||  ||||||  |||| ||||||||||| |||||  | ||||||||||||||||||||||||||||  ||||| ||||| || ||| |||||||||| ||||||||||| ||||||
gtatgtggcaattcaactcatgtacaat----actaagatactgg---ttgtatataacattgctcactaaccatgtctttgtgctac--tcagGGGAAATGGTGCTAGTGTATTAAGAATTGTTCCTTATGCTGCATTACATTATATGGCGTATGAACGATACAGGTGTTGGATCTTGAATAACTGCCCCTCA

upper sequence: GRMZM2G145019_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g01060.t01 (Vitis vinifera), 3'ss of exon 2
gtatgtagcaatttgaatattgcattatttgcactgaatcatcaagattaggatataatattgattactaaccttgtattgatgctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA
       | || |   |  ||     ||||  |||    | |     ||       || ||   || |  | ||| |  | |   |  |||||||||||||||||| |||||  |  | ||||| || ||||| || |||||||| ||| ||||||||| |||| || | ||||| ||||| ||||| ||  | 
-------gtaagtctgaagttattcaatttttact----ctttgttgttttccccaaaaatgtttttcctaacttatgctta-attgtcttcagAGGAAATGGTGCTAGTGTTCTTCGTATTGTACCCTATGCAGCCTTACATTTTATGACATATGAGCAGTACAGGAGCTGGATCTTGAACAACTGCCCTGCC
















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|148961379|gb|EE012117.2|EE012117
EST:     AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAA                         AGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
genomic: AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
EST: gi|91874232|gb|EB404189.1|EB404189
EST:     AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAA                         AGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
genomic: AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
EST: gi|149113164|gb|EE191537.2|EE191537
EST:     AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAA                         AGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
genomic: AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
EST: gi|91055638|gb|EB166056.1|EB166056
EST:     AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAA                         AGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
genomic: AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
EST: gi|211323164|gb|FL255036.1|FL255036
EST:     AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAA                         AGGAAATGGTGC-AGTGTGATGAGAATTGTTCCTTATGCTGCATTACAT
genomic: AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACAT
EST: gi|149098490|gb|EE184470.2|EE184470
EST:     AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAA                         AGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT
genomic: AAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTT

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: 43 (upstream exon), 35 (downstream exon)
Score: 11

ACCAGAACAAATGAGTTTGGGTCTCTTGGAGTTCTCAAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 26

ACCAGAACAAATGAGTTTGGGTCTCTTGGAGTTCTCAAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 29

ACCAGAACAAATGAGTTTGGGTCTCTTGGAGTTCTCAAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 25

ACCAGAACAAATGAGTTTGGGTCTCTTGGAGTTCTCAAATCATTGAAGAAACTGAGACAACTTGATGGAGTCATGGGGTTTTACAAgtatgtagca ... ctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcaagattaggatataatattgattactaaccttgtattgatgctaccttcagAGGAAATGGTGCCAGTGTGATGAGAATTGTTCCTTATGCTGCATTACATTTCATGGCATATGAGCGGTACCGGTGTTGGATTTTGAATAACTGTCCCTCA
                                             ctaccttc  CT-rich tract
       attaggatataatatt  TA-rich tract