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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttcggagtcttctttaatccaactctccatctcagatccatcttatatcttcgaaagagaccctgaaacatcattggcaatcaacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG

Basic information

species Zea mays
transcript GRMZM2G094959_T05
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094959_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g47780.1 (Oryza sativa), 3'ss of exon 9
gtaatgttcggagtc-ttctttaatccaactctccatctcagatccatcttatatcttcgaaagagaccctgaaacatcattggcaatcaacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG
||    | | |||   | ||| | |    || || |  | | | |  |   || |||   |  |||| ||| |     |||    |   ||| ||||||| || |||||||||||||||||||| || ||||| || |||||||||||| ||||||| |
gtgcgttcctgagcagtgcttcacttttcctatcgaaatgaaacctgtggaatttct--aagtgagatcctta-----cataaagagctaacctctcagGTCACCAGCGTTGGGTTTGGGACTGCGTATTCTCAGTAGATGGTGCTTATTTGATAACTG

upper sequence: GRMZM2G094959_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv08s0007g08080.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------gtaatgttcggagtcttctttaatc-caactctccatctcagatccatcttatatc--ttcgaaagagaccctgaaacatcattggcaatcaacttctc-agGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG
                          ||  |||| |   |||  |||  |    ||| |  ||  |||||    ||||||||  |  |   ||||   |||  | | | |||   |  ||||||| ||| |||||||| ||||| ||||||||||| ||||| || |||||||| ||||| || ||||
gtatttatcggagcctcatataagtagttttgtttgttctctggtttgtttgtcactgtaaataccagatg-gccttatatcagtctgtctgagatattga--cgttaatggttgt--acttctctagGACATCAGCGCTGGGTGTGGGACTGTGTTTTCTCTGTGGATGGTGCCTATCTTATCACAG
















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|91874782|gb|EB404739.1|EB404739
EST:     TGTAAAGATTTGGAATGTCGATGGCTTCCAGTTGGAAAGAACTTTAGTCG                         GCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATC
genomic: TGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCGgtaatgttcg ... aacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATC
EST: gi|211318270|gb|FL106362.1|FL106362
EST:     TGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCG                         GCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATC
genomic: TGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCGgtaatgttcg ... aacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATC
EST: gi|32843831|gb|CD983512.1|CD983512
EST:     TGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCG                         GCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATC
genomic: TGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCGgtaatgttcg ... aacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATC

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), 49 (downstream exon)
Score: 105

GTATCTTGCCACAGCATCATCTGACCGCACTGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCGgtaatgttcg ... aacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

GTATCTTGCCACAGCATCATCTGACCGCACTGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCGgtaatgttcg ... aacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 54

GTATCTTGCCACAGCATCATCTGACCGCACTGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCGgtaatgttcg ... aacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

GTATCTTGCCACAGCATCATCTGACCGCACTGTAAAGATTTGGAATGTCGATGGCTTCAAGTTGGAAAGAACTTTAGTCGgtaatgttcg ... aacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatcttatatcttcgaaagagaccctgaaacatcattggcaatcaacttctcagGCCATCAGCGTTGGGTTTGGGACTGTGTCTTCTCCGTCGATGGTGCTTATCTGATAACAG
                                               cttctc  CT-rich tract
     ttatatctt  TA-rich tract