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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttttcaaattctctccatgcgtgcacatattaactttagatgaatgataacatctctgtgttcctgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAATTTTCTTATATCTATGAAGGCAGACCTAAGACAAACTCAGGTTTATTCA

Basic information

species Zea mays
transcript GRMZM2G017584_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017584_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g35130.1 (Oryza sativa), 3'ss of exon 2
gtagtttttcaaattct-ctccatgcgtgcacatattaactttagatgaatgataacatctctgtgttcctgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAATTTTCTTATATCTATGAAGGCAGACCTAAGACAAACTCAGGTTTATTCA
||| ||||    || || |    |   |     | | |  |||| || |    | || |  |||| || || |||||||||  || || ||  || ||   || |||||  || | |||||||  |||||||||||||||||||||||||| ||||||||||||||||| ||    ||||
gtaattttgactatcctgcaatctctctaggtgtgtcacatttatatcagct-tgacgttgctgtttttcttattggtagGCAAATTGCACTGCATTCGCTGATTTCAAGAGATTGTGGATGGCAAAGAAATTTTCTTATATCTATGAAGGAAGACCTAAGACAAACTCTGGCGCTTTCA
















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|211059012|gb|FL008172.1|FL008172
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|211059010|gb|FL008170.1|FL008170
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCA
EST: gi|93014337|gb|EB639857.1|EB639857
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|71326301|gb|DR799839.1|DR799839
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|211059016|gb|FL008176.1|FL008176
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|211059013|gb|FL008173.1|FL008173
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|148954016|gb|EC899414.2|EC899414
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|86469976|gb|DY236346.1|DY236346
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCAAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|211059011|gb|FL008171.1|FL008171
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTTGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|78116765|gb|DV535152.1|DV535152
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|30087147|gb|CB885355.1|CB885355
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|211059014|gb|FL008174.1|FL008174
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
EST: gi|31910413|gb|CD651411.1|CD651411
EST:     TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAG                         GAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA
genomic: TTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAA

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), 42 (downstream exon)
Score: 36

TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAATTTTCTTATATCTATGAAGGCAGACCTAAGACAAACTCAGGTTTATTCA


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 22

TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAATTTTCTTATATCTATGAAGGCAGACCTAAGACAAACTCAGGTTTATTCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 17

TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAATTTTCTTATATCTATGAAGGCAGACCTAAGACAAACTCAGGTTTATTCA


Block sizes: 48 (upstream exon), 30 (downstream exon)
Score: 8

TTTGAGGCTTGGCCATGCCTTTAAATATAGATATTGATCTGTTCAAGCTGGATATTGATGAGCTGATAGCTGATTATTCCAAGgtagtttttc ... tgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAATTTTCTTATATCTATGAAGGCAGACCTAAGACAAACTCAGGTTTATTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgcacatattaactttagatgaatgataacatctctgtgttcctgattggtagGAGAACTGTACATCACTCTTCGAATTCAAACGAGTATGGATGGGCAAGAAATTTTCTTATATCTATGAAGGCAGACCTAAGACAAACTCAGGTTTATTCA
                                       tgttcct  CT-rich tract
       atattaactttagat  TA-rich tract