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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacagagtcccgcccgcacggggcattcttctcgcctcactactgctttgctgctgttcgcttagctgacccccgccggctgttgttcgctccgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG

Basic information

species Zea mays
transcript GRMZM2G089259_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089259_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g07912.1 (Oryza sativa), 3'ss of exon 1
--------------------------gtgacagagtcccgcccgca-----cggggcatt-cttctcgcctcactactgctttgct------gctgttcgcttagctgacc---cccgccggctgttgttcgctccgcac----cgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG
                          |   |    |||| || ||      ||  ||||| |   |   | ||| | || || |||       ||  |    | | | |||        |  |  | | | ||| |          ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||
gtaaggtatcccaaacacacacactcgcttcgctttccccccggcttgatccgatgcattgcaagtaatcgcacgattgattggcttagagtactacttttctcgatcaccaaatttttctcccttcgcttgcttcatgtgttgtccagTGGCTGCGCAAGACGAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG
















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|74237070|gb|DT644984.1|DT644984
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|50337271|gb|CO532397.1|CO532397
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211183324|gb|FK979377.1|FK979377
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|87157614|gb|DY402403.1|DY402403
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|71428557|gb|DR809607.1|DR809607
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|94475718|gb|EB704676.1|EB704676
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211180921|gb|FK979369.1|FK979369
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|50336816|gb|CO531942.1|CO531942
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211183319|gb|FK979372.1|FK979372
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211180923|gb|FK979371.1|FK979371
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211183323|gb|FK979376.1|FK979376
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|22546168|gb|BU098479.1|BU098479
EST:     CGCTGGCCTTGGCTTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: CGCT-GCC-T-GC-TTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|71321201|gb|DR797302.1|DR797302
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|71329466|gb|DR801453.1|DR801453
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211183322|gb|FK979375.1|FK979375
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|87157722|gb|DY402511.1|DY402511
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|148957093|gb|EC903064.2|EC903064
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|22819833|gb|BU499923.1|BU499923
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|37421156|gb|CF648275.1|CF648275
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211226258|gb|FL422663.1|FL422663
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211183328|gb|FK979381.1|FK979381
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|71428023|gb|DR809073.1|DR809073
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|76012907|gb|DT940077.1|DT940077
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|26558674|gb|CA830909.1|CA830909
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|211180922|gb|FK979370.1|FK979370
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGTTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|33466850|gb|CF243899.1|CF243899
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
EST: gi|148994788|gb|EE034233.2|EE034233
EST:     TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAG                         TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC
genomic: TGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATC

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), 48 (downstream exon)
Score: 164

GTCGCTGGCGGAGACGCCCACCTGGTCCGTGGCAACCGTCACCACGCTCATGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 37

GTCGCTGGCGGAGACGCCCACCTGGTCCGTGGCAACCGTCACCACGCTCATGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG


Block sizes: 32 (upstream exon), 48 (downstream exon)
Score: 10

GTCGCTGGCGGAGACGCCCACCTGGTCCGTGGCAACCGTCACCACGCTCATGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 134

GTCGCTGGCGGAGACGCCCACCTGGTCCGTGGCAACCGTCACCACGCTCATGGTCGCTGCCTGCTTCCTCGTCGAGCGCTCCCTCTCGCGCTTCGCCAAGgtgacagagt ... cgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgctgttcgcttagctgacccccgccggctgttgttcgctccgcaccgcagTGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG
                agctgac  putative branch site (score: 134)
                                      ttcgctcc  putative PPT