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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcttccttaaacctttgcagattcacgtatgtgtgtgtgcgcgcgcgtgcacgcgtgtgtaaaacaaaagtgacatgatgtttgtgtgttcatcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAGCAGCCCGCAGTTGAATCAAGT

Basic information

species Zea mays
transcript GRMZM2G023715_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023715_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g21230.1 (Oryza sativa), 3'ss of exon 11
gtaagtttcttccttaaacctttgcagattcacgtatgtgtgtgtgcgcgcgcgtgcacgcgtgtgtaaaacaaaagtgacatgat---gtttgtg-tgttcatcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAGCAGCCCGCAGTTGAATCAAGT
|||||| |  |||||    ||     |  ||  |  |  |    ||| | | | ||   || |    ||||  ||  |||| ||||    | |||| || |  ||||||||||||||||| || |||||||| |||||||| |||||||  ||||| |||||| |||| |||||| | |||||
gtaagtgttctcctt----ctccagtgcctccagcttcagaacatgctctcacatgtg-gcataaccaaaa--aacctgacctgatcatctctgtgatgctgttcatcaagGATCATACAATCCGGGAGGCTTTACGGCACGGTGCCGATGAGGCTGTTCAGCGGCCCACAGTTGCAGCAAGT
















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|148933999|gb|EC878000.2|EC878000
EST:     CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTT                         GATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
genomic: CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
EST: gi|76291830|gb|DV031398.1|DV031398
EST:     CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTT                         GATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
genomic: CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
EST: gi|71768120|gb|DR966057.1|DR966057
EST:     CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTT                         GATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
genomic: CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
EST: gi|148981983|gb|EE028043.2|EE028043
EST:     CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTT                         GATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
genomic: CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
EST: gi|148989785|gb|EE031798.2|EE031798
EST:     CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTT                         GATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG
genomic: CCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAG

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: 38 (upstream exon), 24 (downstream exon)
Score: 2

CGACCTGAGCAACAACACATTTGATCCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAGCAGCCCGCAGTTGAATCAAGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

CGACCTGAGCAACAACACATTTGATCCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAGCAGCCCGCAGTTGAATCAAGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 90

CGACCTGAGCAACAACACATTTGATCCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAGCAGCCCGCAGTTGAATCAAGT


Block sizes: 38 (upstream exon), 41 (downstream exon)
Score: 15

CGACCTGAGCAACAACACATTTGATCCTTCACCATGCCCGGCGTGGTTTTGGAGGCTGCCACAGCTCTCAGCTTTgtaagtttct ... catcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAGCAGCCCGCAGTTGAATCAAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgcacgcgtgtgtaaaacaaaagtgacatgatgtttgtgtgttcatcatcaagGATCATACAGTCTGGGAGGCTCTACGGCACCGTGCCGACAAGGCTTTTCAGCAGCCCGCAGTTGAATCAAGT
              taaaacaaaa  TA-rich tract