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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattcgcacacttgcctctattgtttttctttctcatatgcttgctttagagaagggggaaaacactaatcgaatgtggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC

Basic information

species Zea mays
transcript GRMZM2G006507_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006507_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 3
gtagattcgcacacttgcctctattgtttttctttctcatatgcttgctttagagaaggggga---aaacactaatcgaatgtggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC
||  | | |  |  |||| ||| ||||||||  |  |||| |  ||  |||||  ||         |    |||    | ||    || ||||||||||||||||| ||||| || |||||||| ||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||||||   ||
gtgaagtagatcgtttgcttctcttgttttttctcatcatgtattttgtttaggaaaataatctttactttctacattactgcatttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTC
















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|18964821|gb|BM661215.1|BM661215
EST:     TGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATAACCAAG                         CTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGC
genomic: TGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATAACCAAGgtagattcgc ... tggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGC




















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: 115

AAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATAACCAAGgtagattcgc ... tggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

AAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATAACCAAGgtagattcgc ... tggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

AAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATAACCAAGgtagattcgc ... tggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

AAGATCGAATGAGGGTTTGAGGCTCATATTTTCGGCAGTTATAGGTATCATGCTGGGTTACCTGTTTGGGATCTCCTTCCCTACAGTCAACATAACCAAGgtagattcgc ... tggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcatatgcttgctttagagaagggggaaaacactaatcgaatgtggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC
                                cactaat  putative branch site (score: 133)