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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCCCATTTTAACCCTCATAATAAACCCCATGGAGCTCCATTTGACGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtactaagcctagtctaagatcctttagatggtacgacagatgtatgtttatgaaatattctctgtatcctaataatgctttgcatgcttatttcag

Basic information

species Zea mays
transcript GRMZM5G891739_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G891739_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g11960.4 (Oryza sativa), 5'ss of exon 3
GTCCCCATTTTAACCCTCATAATAAACCCCATGGAGCTCCATTTGACGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtactaagcctagtc--------taagatcctttaga----tggtacgacagatgtatgtttatgaaatattctctgtatcctaataatgctttgcatgcttatttcag
| ||||||||||| ||||| |||||  ||||||| || |||| ||| || ||| ||||| |||||||||||||||| |||||||||||  ||||||||||| |||  | |  | |        ||||| | || ||     |    | |   |  | |||  || || |  | | ||| | | |||||| | |  | |  || || |||
GGCCCCATTTTAATCCTCACAATAAGTCCCATGGGGCACCATCTGATGATGAAAGACATGTGGGCGACCTGGGAAACATAGTAGCCAACAAAGATGgttagcactctgtcaggccgtctacattaagacctttgaggcaactaacgcaaagaaactttgtaaattaattcatgtgtgtctaccaataatacatcacctttttgttccag
















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|37381407|gb|CF627586.1|CF627586
EST:     CGACGAACGACATTTGGGCGACCTGGGAAACATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|4804563|gb|AI665586.2|AI665586
EST:     CGATGAACGACATTTGGGCGACCTGGGAAACATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|10697633|gb|BE997357.1|BE997357
EST:     GCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: GCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|67039156|gb|CO465411.1|CO465411
EST:     CGATGAACGACATTTGGGCGACCTGGGAAACATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|211127614|gb|FL312983.1|FL312983
EST:     CGATGAACGACATTTGGGCGACCTGGGAAACATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|211400090|gb|FL367035.1|FL367035
EST:     CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|211279556|gb|FL330408.1|FL330408
EST:     CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|211437458|gb|FL316488.1|FL316488
EST:     CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|78027318|gb|DV495705.1|DV495705
EST:     CGATGAACGACATTTGGGCGACCTGGGAAACATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|211462831|gb|FL343053.1|FL343053
EST:     CGATGAACGACATTTGGGCGACCTGGGAAACATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|47962526|gb|CN845235.1|CN845235
EST:     CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGGCTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|211383533|gb|FL339775.1|FL339775
EST:     CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG
EST: gi|45568100|gb|CK985902.1|CK985902
EST:     CGACGAACGACATTTGGGCGACCTGGGAAACATAGTAGCCAATGAAGATG                         GAGATGCAGAAGTGTTCATAAGAGACTTACAG
genomic: CGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG

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: 47 (upstream exon), 32 (downstream exon)
Score: 53

GTCCCCATTTTAACCCTCATAATAAACCCCATGGAGCTCCATTTGACGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG


Block sizes: 48 (upstream exon), 32 (downstream exon)
Score: 120

GTCCCCATTTTAACCCTCATAATAAACCCCATGGAGCTCCATTTGACGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG


Block sizes: 47 (upstream exon), 32 (downstream exon)
Score: 89

GTCCCCATTTTAACCCTCATAATAAACCCCATGGAGCTCCATTTGACGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG


Block sizes: 46 (upstream exon), 32 (downstream exon)
Score: 65

GTCCCCATTTTAACCCTCATAATAAACCCCATGGAGCTCCATTTGACGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtacta ... cttatttcagGAGATGCAGAAGTGTTCATAAGAGACTTACAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCCCATTTTAACCCTCATAATAAACCCCATGGAGCTCCATTTGACGACGAACGACATTTGGGCGACCTGGGAAATATAGTAGCCAATGAAGATGgttagtactaagcctagtctaagatcctttagatggtacgacagatgtatgtttatgaaatattctctgtatcctaataatgctttgcatgcttatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG