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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggttagtttcttaccttctactaaaagaattaatgaaatcattacatggtttgatatttgtgaattaatgtatactattgcttaagttggttacctttgaacggatgtattagtctagcaaacaattttgtccacttttcattttctgactagtaattggcagGCATCTCACAGGTTGTAGAAGGTGACTTAGTGTATAACAAAGAATGCCCTTCAGAAGAATCAACTTCCGTAGATATTCTGGAAACTGATGATGACCATAC

Basic information

species Zea mays
transcript GRMZM2G096553_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096553_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os05g43374.1 (Oryza sativa), 3'ss of exon 8
----gtatggttagtttcttaccttctactaaaagaattaatgaaatcattacatggtttgatatttgtgaattaatgtatactattgcttaagttggtta--cctttgaacggatgta--ttagtctagcaaacaattttgtccacttttcatttt---ctgactagt--aattggcagGCATCTCACAGGTTGTAGAAGGTGACTTAGTGTATAACAAAGAATGCCCTTCAGAAGAATCAACTTCCGTAGATATTCTGGAAACTGATGATGACCATAC
    ||    ||  |   |   |  ||||| |  |  ||| |  |||||| |    |||||||| || |    ||| |  ||   |||      ||  | |  | | | | |   ||||  ||  | | |  |||   | | | | | || |   ||   || ||| ||  | ||| ||||||| || |||| |||||||||||||||||| |||| ||||||   |||| | | |||| ||||||| || |||| |   ||| ||   |||||||| | 
gtcagtgcacttcatccttctacagctactca--gttttagttgaatcatgatgcagtttgataattttctgataacggctaaccttgacctttttcttcaggcgtgttaccttttgtagttttatatggtgaacttctcttttcccattcctccttatgctaactggtgtacttgacagGCATTTCGCAGGCTGTAGAAGGTGACTTAGTTTATAGCAAAGAGCCCCCTCCTGGAGAAGCAACTTCAGTTGATACTTCAGAACCTTGCGATGACCAAAT
















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|31353291|gb|CD437648.1|CD437648
EST:     AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAA                         GTATGGCATCTCACAGGTTGTAGAACGTGACTT
genomic: AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAgtatggttag ... taattggcagG-----CATCTCACAGGTTGTAGAAGGTGACTT
EST: gi|211061095|gb|FL320235.1|FL320235
EST:     AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAGTA                       
genomic: AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGG-AAA--Agtatggttag ... taattggc
EST: gi|211061095|gb|FL320235.1|FL320235
EST:     AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAGTA                       
genomic: AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGG-AAA--Agtatggttag ... taattggc
EST: gi|211061095|gb|FL320235.1|FL320235
EST:     AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAGTA                       
genomic: AGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGG-AAA--Agtatggttag ... taattggc

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: 618

GTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAgtatggttag ... taattggcagGCATCTCACAGGTTGTAGAAGGTGACTTAGTGTATAACAAAGAATGCCCTTCAGAAGAATCAACTTCCGTAGATATTCTGGAAACTGATGATGACCATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 156

GTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAgtatggttag ... taattggcagGCATCTCACAGGTTGTAGAAGGTGACTTAGTGTATAACAAAGAATGCCCTTCAGAAGAATCAACTTCCGTAGATATTCTGGAAACTGATGATGACCATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

GTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAgtatggttag ... taattggcagGCATCTCACAGGTTGTAGAAGGTGACTTAGTGTATAACAAAGAATGCCCTTCAGAAGAATCAACTTCCGTAGATATTCTGGAAACTGATGATGACCATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 327

GTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAgtatggttag ... taattggcagGCATCTCACAGGTTGTAGAAGGTGACTTAGTGTATAACAAAGAATGCCCTTCAGAAGAATCAACTTCCGTAGATATTCTGGAAACTGATGATGACCATAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagtctagcaaacaattttgtccacttttcattttctgactagtaattggcagGCATCTCACAGGTTGTAGAAGGTGACTTAGTGTATAACAAAGAATGCCCTTCAGAAGAATCAACTTCCGTAGATATTCTGGAAACTGATGATGACCATAC
                                   ttctgac  putative branch site (score: 327)
           aaacaatttt  TA-rich tract