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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcctcaacagtatcttaaccgaattatttgagtctcagtaacctcgatctaatcatttgatattctcctctccag

Basic information

species Zea mays
transcript GRMZM2G091151_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091151_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 5'ss of exon 8
TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcctcaacagtatcttaaccgaatta-----tttgagtct-cagtaacctcgatct----aatcatttgatattctcctctccag
|||| ||||||||||| |||||||| ||| |||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| ||||| | |||||| |    || || |     ||     |||| | || ||||      |  ||    ||||||||   ||||     |  ||
TACGCTCAAAGTATGATCTCATAGCCAACGTTGTCCATGATGGCAAGCCAGGCGAGGGATGTTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCTTGgtatgctcctcagcttattcctagcatgggtatttattttgtgcctgcagttgagagggccttgtaaatcattttccattccttattttag

upper sequence: GRMZM2G091151_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G22190.1 (Glycine max), 5'ss of exon 9
TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttc-----ctcaacagtatcttaaccgaattatttgagtctcagtaacctcg-----atctaatcat--------ttgatattct-cctctccag
| ||  | || |||||  | || || ||  |||| ||||||||||||||||| || |||| ||| || |||||||| || || |||||||||||    ||||| ||||     ||    |  ||   ||   || |   | | ||| | |             | |||  ||         | |||   |   | |  ||
TGCGAACTAAATATGATTTGATTGCTAATGTTGTTCATGATGGCAAACCTGGTGAAGGATTCTATAGGGTATTTGTGCAACGCAAATCAGAAGAACTATGgtaagttctaattctttgtaagataaaaaaaaaaatgcatcaatctgaatggatgtatggatgtttaacaatgatgagggctaataccttgtttttttag
















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|31250431|gb|CD219455.1|CD219455
EST:     GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
EST: gi|211436060|gb|FL473030.1|FL473030
EST:     GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
EST: gi|8102816|gb|AW927496.1|AW927496
EST:     GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
EST: gi|60348304|gb|DN215277.1|DN215277
EST:     GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
EST: gi|12046728|gb|BF728867.1|BF728867
EST:     TGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: TGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
EST: gi|22491133|gb|BU051056.1|BU051056
EST:     GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
EST: gi|76927561|gb|DV171298.1|DV171298
EST:     GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
EST: gi|8102817|gb|AW927497.1|AW927497
EST:     GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTG                         GTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC
genomic: GGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGC

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: 152

TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGCTCTCTCAGAAACCTACATGCAAATATACGAGCAACACGAATGAGTAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 101

TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGCTCTCTCAGAAACCTACATGCAAATATACGAGCAACACGAATGAGTAATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 88

TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGCTCTCTCAGAAACCTACATGCAAATATACGAGCAACACGAATGAGTAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcct ... tcctctccagGTATGAGATGCAGGATCTCCATGTTACTGAGACCCTTCCTCAAATGGTTGCTCTCTCAGAAACCTACATGCAAATATACGAGCAACACGAATGAGTAATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACGTTCAAAGTATGACCTCATAGCAAACATTGTCCATGATGGCAAACCTGGCGAGGGATGCTACAGAGTATTTGTACAGCGGAAATCAGAAGAGGCCTGgtacgttcctcaacagtatcttaaccgaattatttgagtctcagtaacctcgatctaatcatttgatattctcctctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG