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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttgccttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG

Basic information

species Zea mays
transcript GRMZM2G109039_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109039_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 3
gtttgcctcttactcctgttggaagtttggctttgtaaaattttctatccgcatgtgtttgacacttg---ccttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG
         |   |||| ||| ||| |   || |||| || | ||| |  |  |||| |||||| |||   | |  | | |||| |||||||| || || ||||| ||||| || ||||| ||||| |||||||||||||| || ||||||||||| ||||||||||||
--------gtgcgtccttttgaaagctca-ctgtgtagaactgtctgt--gtttgtgcttgacagttgacacttgtgtacagGAATGCAAACCGACTGAAAAAGGCGGGATGTATTATGAATTTAGGCGAAATACTAGATCAGTAAAATCAACTATACTACATTTTCAG
















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|211166255|gb|FL395975.1|FL395975
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|211150113|gb|FL386529.1|FL386529
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20301188|gb|BQ164131.1|BQ164131
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20301181|gb|BQ164124.1|BQ164124
EST:     AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20300911|gb|BQ163854.1|BQ163854
EST:     AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCANCAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
EST: gi|20300918|gb|BQ163861.1|BQ163861
EST:     AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAG                         GATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT
genomic: AAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAAT

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: 471

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 478

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 596

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 484

GGAGCAGATAAACATAACCCGTAAAAAATACAGACAGTCCAGATTAGAACAGTACAAAAATTATGAGAATGTACCTAACTCTGGAGAAGAAGCTATGAAGgtttgcctct ... cttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttggctttgtaaaattttctatccgcatgtgtttgacacttgccttggaatagGATTGCAAACCAACAGAGAAAGGTGGGATATACTATGAGTTTAGACGAAATACTAGATCGGTTAAATCAACTATTCTACATTTTCAG
                                gtttgac  putative branch site (score: 484)
                                        cttgcctt  CT-rich tract
       tttgtaaaattttcta  TA-rich tract