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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgcgaaagcttgtacttgagtaacttaaatgtcattttctatcatgttctaacgcacacactatcgttttttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT

Basic information

species Zea mays
transcript GRMZM2G137236_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 15
gtaagtcgcgaaagcttgtacttgagtaacttaaa-tgtcattttctatcatgttctaacgcacacactatcgttttttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT
||||||    ||||| |   ||| | | ||| |   | || | ||||||| |    | |   |   || ||    ||||| |||||| | |||||||| ||||||||||| || || |||||||||||| |||||||||| ||||| |||||||| |||||||| ||||||||||| |||||||| 
gtaagttttaaaagcctc--cttaatttactaatgctatcttcttctatccttgcgtgatatatgtaccatgaaattttc-atcagGACGAGTACTGTCGCTATTCTTCTGTCGACTTATGCCAAGATACTGATGCACACACAACCCCCTGATGTGGGACTGCAGCAACAAATCCTGACAATATTC

upper sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 15
gtaagt-cgcgaaagcttgtacttgag----taacttaaatgtcattttctatcatgttctaacgcacacactatcgttttttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT
|||||  | |  |  |||| |  ||      |  |||| | ||  |   ||   ||  |   |  |  | |  |    || | |  ||||| |   ||| ||  |||||||||| ||||| ||||| ||||| |||||||||||||||||  | ||    | ||| ||  | || ||     ||||||| 
gtaagagctcttagccttgcatctgttgtcttttcttatacgttctgcccttcaatcctaggat-cttaaaacacatattgtactttcagGACTTCTACAGTTCCTATTCTTCTTTCAACATATGCTAAGATTTTGATGCACACTCAACCCTCAGACCCAGAACTACAGAATCAGATTTGGGCAATATTC
















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|101401386|gb|EB822370.1|EB822370
EST:     TGCTATTATAAATGATAAACTTCCTACAGTATC                         GGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCA
genomic: TGCTATTATAAATGATAAACTTCCTACAGTATCgtaagtcgcg ... tttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCA




















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: 117

CCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTACAGTATCgtaagtcgcg ... tttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 92

CCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTACAGTATCgtaagtcgcg ... tttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

CCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTACAGTATCgtaagtcgcg ... tttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 122

CCTACCTTCTTGGGGAGTATGGACATCTTTTGGCCCGGAGACCTGGCTGTAGCCCTAAGGAATTGTTTGCTATTATAAATGATAAACTTCCTACAGTATCgtaagtcgcg ... tttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaatgtcattttctatcatgttctaacgcacacactatcgttttttccatcagGGCAAGTACTGTAGCTATTCTTCTCTCAACCTATGCCAAGATATTGATGCACACTCAACCTCCTGATGTTGGACTGCAACAACAAATCCTCACAATATTT
                      ttctaac  putative branch site (score: 122)
                                    ctatcgttttttcc  putative PPT
         attttctat  TA-rich tract