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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttttaatctgaatttcagatgttctcctattgataatgcctctgttactggataacttggatcaatgtacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G25110.1 (Glycine max), 3'ss of exon 9
gtttgttcttttaatctgaatttcagatgt-tctcctattgataatgcctctgttactggataacttggatcaatgtacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG
    ||  | | | | |   | |   |||| | |  ||||  |   | ||  |    |  |||||    |||||| |    |   |||| | |||||||| |||||||||||||| || ||||||||||||||  | ||||| || || |||||||| || |||||||||||    || || |  ||||
----gtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcttggccctttcataac----atcaattttt--ttcaccagAGATATGGTCCTCCTCCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGAGCTAGTTTTGGTTACCATCCCGGTGGCTGGG

upper sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA15G07760.1 (Glycine max), 3'ss of exon 9
gtttgttcttttaatctgaatttcagatgttctcctattgataatgcctctgttactggataacttggatcaatg--tacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG
         |   ||   |   ||   ||||    | || ||| |   |||||| ||||     ||    || |   ||   | || ||| | |||||||| || ||||| ||||| || ||||||||||| || || ||||| |||||||||||||| || || |||||||||   || || |  ||||
--------gtaatattatagcctcttctgttgcatttttcatattat-tctgttcctggcctttttaccccattaaatatgttttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAGATCCCTGGACTGAATGCTCCAATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG

upper sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA07G31350.1 (Glycine max), 3'ss of exon 5
gtttgttcttttaatctgaatttcagatgt-tctcctattgataatgcctctgttactggataacttggatcaatgtacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG
    ||  | | | | |   | |   |||| | |  ||||  |   | |   |    |  ||||| |  ||   | | ||            |||||||| ||| |||||||||| || ||||||||||||||  | ||||| || || |||||||| || |||||||||||    || || |  |   
----gtaatatcagtgtctttgtggcatgtatgttgtattcttctggtcctggccctttcataacatcaattttttt-caccagagGTATTGTATGGTCCTCCTTCATCTTATCCTCATCTGAAGATCCCAGGCTTGAATGCTCCCATTCCCCCTGGGGCAAGTTTTGGTTACCATCCTGGTGGCT---

upper sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 9
gtttgttcttttaatctgaatttcagatgttctcctattgataatgcctctgttactggataacttggatcaatgtacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG
         |   ||   |   ||   ||||    | || ||| |   |   |  |    | ||     | ||| |  | | || ||| | |||||||| || ||||| ||||| || ||||| ||||| || || ||||| || ||||||||||| || || |||||||||   || || |  ||||
--------gtaatattatagcgtcttctgttgcatttttcatattctgttactggccttttgaccccattaaatatg-attttttcagAGATATGGTCCTCCACCATCATATCCTCATCTGAAAATCCCTGGACTGAATGCTCCTATCCCCCCTGGAGCTAGCTTTGGTTATCATCCTGGTGGATGGG

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|51592523|gb|CV071669.1|CV071669
EST:     CTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGCAG                         CGCTAGGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAAT
genomic: CTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGCAGgtttgttctt ... aatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAAT




















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: 479

TAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGCAGgtttgttctt ... aatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 220

TAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGCAGgtttgttctt ... aatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 343

TAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGCAGgtttgttctt ... aatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 267

TAAACTGAGGGAAATGAAGCCAGGCATGCTGTCTCGTGAGCTTAAAGATGCTCTTGGTATGCCTGATGGCGCCCCTCCCCCATGGCTTATAAACATGCAGgtttgttctt ... aatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctattgataatgcctctgttactggataacttggatcaatgtacaatgttccagCGCTATGGTCCACCTCCATCTTATCCCCAACTGAAGATCCCAGGTCTAAATGCCCCAATCCCCCCTGGTGCCAGTTTTGGTTATAGACCAGGGGAGTGGG
                        ggataac  putative branch site (score: 267)
     tgataat  TA-rich tract