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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttgcaagcgtccagtcttaaagctccaaacatatacagacagttttctttcttttccatcctgctttatttctagcattaactttattttattttcagattgaatccaagaatagataatgatacaacagtattgttggtaatatgcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGGTGTTACTTCTAAACTACATAGGAGGTGCTACAAACACAGGAATTGTTTC

Basic information

species Zea mays
transcript GRMZM2G039396_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039396_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 3'ss of exon 7
gtatttcttgcaagcgtccagtctta--aagctccaaacatatacagacagttttctttcttttccatcctgctttatttctagcattaactttattttattttcagattgaatccaagaatagataatgatacaacagtattgttggtaatatgcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGGTGTTACTTCTAAACTACATAGGAGGTGCTACAAACACAGGAATTGTTTC
    | |||  | |  | ||  ||||  |  || | |||||||| |   | |  |||||||| || |   ||| ||  || | | ||||| |||  ||                          ||| || |   |||   |||| |||| |||  || | ||||||||||||| || || ||||||||||||||||||||||| |  || |||||||||||||| ||||||||||||||| ||||||| ||||| ||||||||
---gtacttataggaattcaaccttattattcttctaacatataaatgaactaatctttcttgtctagtttgcatttattgtgg-attaagtttggtt--------------------------atattgttcttacaagtttgt-ggtattat-tttgtatagGAACAATATATAGCTCATCACTCTTTCCAAATCGTGCTCCAGCTGGAAGGGTGTTACTTCTGAACTACATAGGAGGTTCTACAAATACAGGGATTGTTTC
















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|76286241|gb|DV025809.1|DV025809
EST:     CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAG                         GAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
genomic: CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
EST: gi|149005348|gb|EE039899.2|EE039899
EST:     CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAG                         GAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
genomic: CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
EST: gi|213183994|gb|FM183521.1|FM183521
EST:     CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCCAGGAGTTGAGACATTAG                         GAACAATATACAGTTCCTCACT
genomic: CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACT
EST: gi|67014942|gb|CO443691.1|CO443691
EST:     CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAG                         GAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
genomic: CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
EST: gi|13237375|gb|BG355389.1|BG355389
EST:     CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAG                         GAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
genomic: CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
EST: gi|78087540|gb|DV515933.1|DV515933
EST:     CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAG                         GAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
genomic: CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
EST: gi|67020129|gb|CO448878.1|CO448878
EST:     CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAG                         GAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG
genomic: CCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGG

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), 45 (downstream exon)
Score: 43

TCGTATCCAAAGGAAGCAATTAGAAAAGAATGCTTAATTGATGGGGAACTCCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGGTGTTACTTCTAAACTACATAGGAGGTGCTACAAACACAGGAATTGTTTC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 104

TCGTATCCAAAGGAAGCAATTAGAAAAGAATGCTTAATTGATGGGGAACTCCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGGTGTTACTTCTAAACTACATAGGAGGTGCTACAAACACAGGAATTGTTTC


Block sizes: 39 (upstream exon), 43 (downstream exon)
Score: 20

TCGTATCCAAAGGAAGCAATTAGAAAAGAATGCTTAATTGATGGGGAACTCCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGGTGTTACTTCTAAACTACATAGGAGGTGCTACAAACACAGGAATTGTTTC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 46

TCGTATCCAAAGGAAGCAATTAGAAAAGAATGCTTAATTGATGGGGAACTCCAGGGCTTTGGCCAGTTGCATCCACGTAGTCAAGGAGTTGAGACATTAGgtatttcttg ... gcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGGTGTTACTTCTAAACTACATAGGAGGTGCTACAAACACAGGAATTGTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatccaagaatagataatgatacaacagtattgttggtaatatgcttttgtagGAACAATATACAGTTCCTCACTCTTTCCAAATCGTGCTCCTGACGGTAGGGTGTTACTTCTAAACTACATAGGAGGTGCTACAAACACAGGAATTGTTTC
                                            tgctttt  CT-rich tract
          aatagataatgata  TA-rich tract