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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaactctactcactctctagagtatgcctctttctgtgttttttagcagtgctgtacttattggacaacaggtctgtttcattctttaaatttgctgcttctctacatgcactctgaattgatattattttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348675_T02 (Zea mays), 3'ss of exon 33
lower sequence: LOC_Os11g42420.1 (Oryza sativa), 3'ss of exon 9
gtgaactctactcac-tctctagagtatgcctctttctg-tgttttttagcagtgctgtacttattgga---caacaggtctgtttcattctt---taa-----atttgctgcttctcta-catgcactctgaattgatattattttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG
|| ||   | |||   | | |  | |||||    || || | |   |||   || ||| | || ||      |  ||  |   || || | ||   ||      |  |  |||||  | | | |  |     |||||||| ||||| |  ||||||| ||||| |||||||| ||||| ||||||||||| ||||||||||||||||||||||||||||||||| ||||||| ||||||||||||||||||
gttaaacatgctcttgtttttgaactatgctctgttgtgctctcaattaatggt-ctgaatttttttattttcttcaaattcattacacttttgtgtagccagcacataatgctttgcaaacctaaatctgaaattgataatatttatgtagAAAATTGCTGAACAAGATGGTGGCCGATATGAGATGGCAGTATATGCTTTACAATGCAGTAACTTAAAGCGTATCTTGCCGATCTGTACTGACTGGGAG
















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|211285653|gb|FL023028.1|FL023028
EST:     TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAG                         AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
genomic: TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
EST: gi|60349063|gb|DN216036.1|DN216036
EST:     TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAG                         AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
genomic: TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
EST: gi|60349063|gb|DN216036.1|DN216036
EST:     TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAG                         AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
genomic: TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
EST: gi|5567060|gb|AI881971.1|AI881971
EST:     TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAG                         AAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
genomic: TTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA
EST: gi|31441055|gb|CD510486.1|CD510486
EST:     ATATTG-GCTTCAGAG                         AAAATCGCTGAGCAAGATGGAGG-CGTTATGAGATGGCTGTATATGCTTTA
genomic: ATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTA

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: 589

CAAAAATGGAAAGTACAGAACACTACAAGCCATGGAATTAGAAAGTGGTGTTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 150

CAAAAATGGAAAGTACAGAACACTACAAGCCATGGAATTAGAAAGTGGTGTTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

CAAAAATGGAAAGTACAGAACACTACAAGCCATGGAATTAGAAAGTGGTGTTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 144

CAAAAATGGAAAGTACAGAACACTACAAGCCATGGAATTAGAAAGTGGTGTTGGGCGGCAGTGGCGTCTTTGGAAATGGGCATCATATTGTGCTTCAGAGgtgaactcta ... attttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttaaatttgctgcttctctacatgcactctgaattgatattattttttcagAAAATCGCTGAGCAAGATGGAGGCCGTTATGAGATGGCTGTATATGCTTTACAATGCAGTAACTTAAAGCGTGTCTTGCCAATCTGTACTGACTGGGAG
                                   aattgat  putative branch site (score: 144)
                                           ttattttttc  CT-rich tract
                               tctgaattgatattat  TA-rich tract