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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcatgtcactcgctgccattgctgatccacagggacacacaccagctagctgtccaagagttttctttttttttatgcttcaatctgttcactttgcttgcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCTCGCCTCACCCCTTCATCAACCTCAAGGGAATCCTT

Basic information

species Zea mays
transcript GRMZM5G879749_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879749_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 4
gtgagtcatgtcactcgctgccattgctgatccacagggacacacaccagctagctgtccaagagttttctttttttttatgcttcaatctgttcactttgcttgcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCTCGCCTCACCCCTTCATCAACCTCAAGGGAATCCTT
    || ||||      ||| |  || |      ||    ||      |      | ||   |  |  |||   |  |      || |||     | |||||     | |  ||| || ||||| ||||||||||||||||||||||| |||| |||| ||||||| ||  | || ||||||||||||||||| ||||||
----gtaatgt-gtaaactggcgatgtt----tgcatcaccatctctgaaactattatctctgcatcatctgactactg-----tccatcaacaaaatttgcacaaattc-tagGACATTACGTTCCCCAGTTGGCAAGGAAGATCGTTGAGTTCAACAAGGCCTCACCATATCCTTTCATCAACCTCAAGGGGATCCTT
















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|116817956|gb|EC860887.1|EC860887
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATTGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|29946821|gb|CB816342.1|CB816342
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|76020009|gb|DT947179.1|DT947179
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|94479697|gb|EB708655.1|EB708655
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|93014934|gb|EB640454.1|EB640454
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|101395266|gb|EB819563.1|EB819563
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|71775053|gb|DR972931.1|DR972931
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 67

CTCAAGACGCGCTGCAGTTCCTGGTCAGCTGGATGTCACGGTTCCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCTCGCCTCACCCCTTCATCAACCTCAAGGGAATCCTT


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 6

CTCAAGACGCGCTGCAGTTCCTGGTCAGCTGGATGTCACGGTTCCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCTCGCCTCACCCCTTCATCAACCTCAAGGGAATCCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 20

CTCAAGACGCGCTGCAGTTCCTGGTCAGCTGGATGTCACGGTTCCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCTCGCCTCACCCCTTCATCAACCTCAAGGGAATCCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagagttttctttttttttatgcttcaatctgttcactttgcttgcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCTCGCCTCACCCCTTCATCAACCTCAAGGGAATCCTT
                                     ctttgcttgcttcc  CT-rich tract
      ttttctttttttttat  TA-rich tract