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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtaaacatgttactcattgtctcaataatatccatttttgtaaagtgtaaactgttctagccatacatgcaagacaattaatttgacaaattttcttttgctgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 12
gttggtaaacatgttactcattgtctca-ataatatccatttttgtaaagtgta--aactgttctagccatacatgcaagacaattaatttgacaaattttcttttgctgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG
||  || ||  | ||  | |||| ||   |  || | ||| |||  ||| ||||  ||| ||||||||| || ||||||| |||| | ||||||| ||||||| |||||  || |||||| || |||||||| |||||||||||||| ||||| |||||||||||||||||||||||||| || || ||| ||||||||||||||||||| |||
gtcagtcaaagtttttattattgacttgtactattttcatattttgaaaatgtattaacagttctagccttatatgcaaggcaatcagtttgacacattttctattgctactcctcagACTGCACAAGATAACATTGATCTGCAGACAACCATCCTTTCTAGATTTGATCTAATCTTTATTGTTAAAGATGTCAGAATGTATGATCAAGACAAG

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 11
gttggtaaacatgttactcattgtctcaataatatc-catttttgtaaagtgtaaactgttctagccatacatgcaagacaattaatttgacaaattttcttttgctgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG
||| | |||  || |||||  |   |    ||||||    ||||    | | |    ||||   || |||     ||||  ||   | ||     |||| || |   | |   ||||| || || || ||||| ||||||||||| || |||||||||||||||||||| ||||| || |||||||| ||||| | ||||   ||||| |||
gtttg-aaatctggtactc--tcctttggcaatatcatggttttcccgattct----tgttt--gcaatattcttaaga-gatgggtgtgtt---tttttttctttggatttgcagACTGCTCAGGACAATATCGATCTGCAGACAACAATTCTTTCTAGATTTGATCTTATCTTCATTGTCAAGGACATCAGGAAGTATTCCCAAGACAAG
















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|32939404|gb|CF044223.1|CF044223
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAG                         ACCGCACAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... tgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGAT
EST: gi|32833256|gb|CD972934.1|CD972934
EST:     CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAG                         ACCGCACAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGAT
genomic: CAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... tgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGAT
EST: gi|22546223|gb|BU098534.1|BU098534
EST:     GATGATCTTAAG                         ACCGCACAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGAT
genomic: GATGATCTTAAGgttggtaaac ... tgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 362

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... tgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... tgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 41

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... tgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 27

AATATCTATTGCCAAAGCTGGCATTACAACAGTACTCAATTCAAGGACTTCAGTTCTTGCAGCTGCCAATCCAATTGCAGGACGCTATGATGATCTTAAGgttggtaaac ... tgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagccatacatgcaagacaattaatttgacaaattttcttttgctgttcatcagACCGCGCAAGATAATATTGATCTGCAGACGACCATTCTTTCTAGATTTGATCTAATCTTTATCGTCAAGGATATCAGAATGTATGATCAAGATAAG
                                  ttttcttttgctgttc  CT-rich tract
                   aattaatttgacaaat  TA-rich tract