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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgatctttgtcacctaaatttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA

Basic information

species Zea mays
transcript GRMZM2G124886_T04
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 16
gtgagttgatctttgtcacctaa-atttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
||||||   |  |||||   ||   | |||  |   |       |   || ||||| || |||  |  ||| ||| ||||||||||||||||||||||||||||||| | |||| |||||||||||||||||||||||||| || || ||||||||||| | | ||||| |||||||||||
gtgagtct-tggttgtctggtatcgtatcatattcggaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACTATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 7
gtgagttgatctttgtcacctaaatttcacttgtagtttttgtacacaag----ttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
    ||   |||| ||   ||    ||   |  || | |     |||||     ||||| || |||  |  ||| ||| |||||||||||||||||||||||||||||||   |||| |||||||||||||||||||||||||| || || ||||||||||| | | ||||| |||||||||||
----gtgagtcttggttgtctggtattgtatcatattctgaagccacaatgaacttctgaggttaacttgttttcttactgcagTGTTGTGGGGTATACTTTACTCCTTACCATGATTGAGTATAAAACACTTGTAATGCGTGGAGACTTCGATCGTGCAAACGCTCTTTTACCATCTATACCA

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
----gtgagtt---gatctttgtcacctaaatttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
    | ||| |   || ||      |   ||| | |||  |  | ||  |  |   | |||     || |    || | |  ||||||||| |||| ||||| ||||| || | |||||| ||||| || ||||||||||||||||| || ||| | ||||||| |||  ||||| | |  || || 
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

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|60337834|gb|DN204807.1|DN204807
EST:     GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAA                         TGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGT
genomic: GGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttgat ... tttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGT




















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: 425

GTTACAACCTTATTTCACTTGGATCGGCCAATGTATTTACTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttgat ... tttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 536

GTTACAACCTTATTTCACTTGGATCGGCCAATGTATTTACTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttgat ... tttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 479

GTTACAACCTTATTTCACTTGGATCGGCCAATGTATTTACTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttgat ... tttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 781

GTTACAACCTTATTTCACTTGGATCGGCCAATGTATTTACTAGGATATCTTGCAAACCAAAGCCGTGTCTATCTTATTGATAAGCAATTTAAgtgagttgat ... tttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttgtagtttttgtacacaagttctgtggctaatgtacttttttattgcagTGTTGTGGGGTATACTTTACTCCTTAGTTTGATCGAGTATAAAACACTTGTAATGCGTGGGGATTTTGATCGTGCAAATGATGTTTTATCATCTATACCA
                               ggctaat  putative branch site (score: 781)
                                         cttttttatt  putative PPT
                                  taatgtacttttttat  TA-rich tract